fbergmann / libsedml Goto Github PK

SED-ML library based on libSBML

License: BSD 2-Clause "Simplified" License

CMake 2.27% C++ 89.69% Python 0.31% C 4.17% Shell 0.04% Batchfile 0.01% SWIG 3.51%

sedml libsbml numl combine

libsedml's Introduction

LibSEDML

Some time ago I developed libSedML a C# library that fully supports SED-ML for SBML as well as CellML models for creation of the description just as for the execution of Simulation Experiments. However, frequently the question to a C++ based library comes up. This project makes use of libSBML XML layer as well as code generation as starting point to produce a library for reading and writing of SED-ML models.

Dependencies

This library requires libSBML to be present, as its XML parsing layer will be used. for that either expat, xerces-c or libXML2 needs to be available. Additionally libSEDML makes use of libnuml. All dependencies are available as git submodule.

Building Python wheels

Since all dependencies are included as submodules, be sure to checkout the project with submodules:

git clone --recurse-submodules https://github.com/fbergmann/libSEDML

Then a build is as easy as:

cd libSEDML
python src/bindings/python/setup.py build

or install, if you prefer. It requires cmake and swig installed.

Building

This library uses CMake to build the library, so from an initial checkout all you would need todo is to run:

mkdir build  
cd build
cmake -DLIBSBML_LIBRARY=< path to libsbml lib> -DLIBSBML_INCLUDE_DIR=< path to includes > ... -DEXTRA_LIBS= < comma separated list of xml libraries> 
make  
make install

Should libSBML be installed in a default location it will be found automatically. Note that you do need to list the xml libraries that libSBML was linked against. In most cases libSBML is compiled against libXML and have compression enabled, so your EXTRA_LIBS would be:

EXTRA_LIBS=xml2;bz2;z;iconv

note the semicolon denoting the listing of several libraries. Of course you could also enter the full path to each individual file, just to give an example, on windows I use:

EXTRA_LIBS=D:/dependencies/lib/expat.lib

for linking against expat and indicating, that libSBML was compiled without compression.

Documentation

API documentation is something to be added and pull requests are happily accepted to improve them. For now a basic doxygen file is provided and documentation can be generated after checkout like so:

PROJECT_NUMBER=2.0.32 doxygen -x libSEDML.doxyfile > Doxyfile && doxygen

This expands the version number in the doxygen file, creates a temporary Doxyfile and runs doxygen with it. After that the generated documentation is available in the ./doc/html folder.

License

This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

libsedml's People

Contributors

Stargazers

Watchers

Forkers

nickerso hsorby bmoreau 0u812 matthiaskoenig opencor vincent-noel sed-ml gmarupilla amdmi3 jonrkarr weiweiai

libsedml's Issues

Having trouble with annotations (in algorithms)

I'm having trouble when trying to use the annotation element as a child of the simulation algorithm. The print_sedml example works fine if I have an empty annotation element present, but as soon as I have children elements in there it segfaults on the mSed->getNamespaces() call as part of the SedBase::readAnnotation::checkAnnotation method.

I haven't checked to see if this is specific to the algorithm class or a general problem with annotations.

(the SED-ML web-tools have no problem and tell me I have a valid SED-ML document.)

Python3 support

Is Python3.x bindings supported?

Thanks.

[libSEDML-0.3.0] libsedmlcsP.dll not compiled

Hi.
On my Fedora 21 x86_64 i'm compiling libSEDML including Python, Ruby, Java, R, Mono, Perl bindings. Ruby library seems successfully compiled just if i use '-Wno-error=unused-value' CXX flag, indeed various warnings prevent building conclusion with -Werror.

csharp library is not compiled because of a lot of CS0246 errors. Please, see full log https://sagitter.fedorapeople.org/libSEDML/libSEDML_log.tar.gz

Regards.

Validation does not check for algorithm on simulation

The following sedml is read without warnings/errors despite missing the algorithm on the simulation. There should be an libsedml.LIBSEDML_SEV_ERROR when reading the file.

SEDML spec: "Each instance of the Simulation class MUST contain one reference to a simulation algorithm"

<?xml version="1.0" encoding="UTF-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
  <listOfSimulations>
    <oneStep id="stepper" step="0.1"/>
  </listOfSimulations>
  <listOfModels>
    <model id="model1" language="urn:sedml:language:sbml.level-3.version-1" source="oscli"/>
  </listOfModels>
  <listOfTasks>
    <task id="task0" modelReference="model1" simulationReference="stepper"/>
    <repeatedTask id="task1" range="x" resetModel="false">
      <listOfRanges>
        <uniformRange id="x" start="0" end="10" numberOfPoints="100" type="linear"/>
      </listOfRanges>
      <listOfChanges>
        <setValue range="x" modelReference="model1" target="/sbml:sbml/sbml:model/descendant::*[@id=&apos;J0_v0&apos;]">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <piecewise>
              <piece>
                <cn type="integer"> 8 </cn>
                <apply>
                  <lt/>
                  <ci> x </ci>
                  <cn type="integer"> 4 </cn>
                </apply>
              </piece>
              <piece>
                <cn> 0.1 </cn>
                <apply>
                  <and/>
                  <apply>
                    <leq/>
                    <cn type="integer"> 4 </cn>
                    <ci> x </ci>
                  </apply>
                  <apply>
                    <lt/>
                    <ci> x </ci>
                    <cn type="integer"> 6 </cn>
                  </apply>
                </apply>
              </piece>
              <otherwise>
                <cn type="integer"> 8 </cn>
              </otherwise>
            </piecewise>
          </math>
        </setValue>
      </listOfChanges>
      <listOfSubTasks>
        <subTask order="0" task="task0"/>
      </listOfSubTasks>
    </repeatedTask>
  </listOfTasks>
  <listOfDataGenerators>
    <dataGenerator id="plot_0_0_0" name="task1.time">
      <listOfVariables>
        <variable id="task1_____time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> task1_____time </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="plot_0_0_1" name="task1.S1">
      <listOfVariables>
        <variable id="task1_____S1" target="/sbml:sbml/sbml:model/descendant::*[@id=&apos;S1&apos;]" taskReference="task1" modelReference="model1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> task1_____S1 </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="plot_0_1_1" name="task1.S2">
      <listOfVariables>
        <variable id="task1_____S2" target="/sbml:sbml/sbml:model/descendant::*[@id=&apos;S2&apos;]" taskReference="task1" modelReference="model1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> task1_____S2 </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="plot_0_2_1" name="task1.J0_v0">
      <listOfVariables>
        <variable id="task1_____J0_v0" target="/sbml:sbml/sbml:model/descendant::*[@id=&apos;J0_v0&apos;]" taskReference="task1" modelReference="model1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> task1_____J0_v0 </ci>
      </math>
    </dataGenerator>
  </listOfDataGenerators>
  <listOfOutputs>
    <plot2D id="plot_0">
      <listOfCurves>
        <curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_0_1"/>
        <curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_1_1"/>
        <curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_2_1"/>
      </listOfCurves>
    </plot2D>
  </listOfOutputs>
</sedML>

Undefined symbols

Hi,

i don't not know what causes these undefined symbols in libsedml.so.0.3.0 library; what do you think?

$ ldd -d -r /usr/lib64/libsedml.so.0.3.0

linux-vdso.so.1 (0x00007ffdbb1f2000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f571bdd1000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f571bbba000)
libc.so.6 => /lib64/libc.so.6 (0x00007f571b7fa000)
libm.so.6 => /lib64/libm.so.6 (0x00007f571b4f2000)
/lib64/ld-linux-x86-64.so.2 (0x00007f571c424000)
undefined symbol: _ZTI8XMLError (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZTI11XMLErrorLog (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStreamlsERKd    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStreamlsERKSs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError17stringForSeverityEj    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces8getIndexESs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces11containsUriESs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _Z8hasBzip2v  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken7getLineEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLTokenC1ERKS_   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces5hasNSERKSsS1_ (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes6getURIEi  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker18isValidInternalSIdESs (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _Z11writeMathMLPK7ASTNodeR15XMLOutputStreamP14SBMLNamespaces  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError10getErrorIdEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken6isTextEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStreamC1EPKcbSsP11XMLErrorLog    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStreamD1Ev   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeC1ERK8XMLToken (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken13getCharactersEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces9getPrefixEi   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError11getSeverityEv  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces9getLengthEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeD1Ev   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14SBMLNamespaces13addNamespacesEPK13XMLNamespaces  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLErrorD1Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker17isCorrectHTMLNodeERK7XMLNode  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes9getPrefixEi   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN19RDFAnnotationParser23hasHistoryRDFAnnotationEPK7XMLNode  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLAttributesD1Ev    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream14writeAttributeERKSsS1_RKb   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLNamespaces6removeERKSs    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _Z7hasZlibv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZlsR15XMLOutputStreamRK13XMLNamespaces   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK7XMLNode5cloneEv  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: safe_strdup   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK4List7getSizeEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode22convertStringToXMLNodeERKSsPK13XMLNamespaces (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK7XMLNode14getNumChildrenEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode11removeChildEj    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker13hasDeclaredNSERK7XMLNodePK13XMLNamespaces (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStreamD1Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK7XMLNode8getIndexERKSs    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes8readIntoERKSsRdP11XMLErrorLogbjj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14SBMLNamespacesC1Ejj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN16OutputCompressor15openGzipOStreamERKSs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLAttributes11setErrorLogEP11XMLErrorLog    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker12isValidXMLIDESs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStream10getVersionEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN9XMLTripleC1ERKSsS1_S1_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN11XMLErrorLog3addERK8XMLError  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK11XMLErrorLog8getErrorEj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes8readIntoERKSsRbP11XMLErrorLogbjj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError7getLineEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeC1ERK9XMLTripleRK13XMLAttributesjj (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK7ASTNode19isWellFormedASTNodeEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker16isAllowedElementERK7XMLNode   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream13setAutoIndentEb (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN4List12transferFromEPS_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode11insertChildEjRKS_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode14removeChildrenEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream14writeAttributeERKSsS1_RKi   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK14XMLInputStream6isGoodEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode8addChildERKS_ (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode22convertXMLNodeToStringEPKS_  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLErrorD2Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces6getURIERKSs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN19RDFAnnotationParser22hasCVTermRDFAnnotationEPK7XMLNode   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces6hasURIERKSs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces5cloneEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes7getNameEi (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN4ListC1Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLAttributesC1Ev    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLNamespacesC1ERKS_ (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLNamespaces3addERKSsS1_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZlsR15XMLOutputStreamRK7XMLNode  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeC1Ev   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker14isValidSBMLSIdESs (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken7getNameEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError19getSeverityAsStringEv  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _Z10readMathMLR14XMLInputStreamRKSs   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK14XMLInputStream7isErrorEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes9getLengthEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError10getMessageEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLTokenC1ERK9XMLTripleRK13XMLAttributesRK13XMLNamespacesjj   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces16getNumNamespacesEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken5isEndEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken13getNamespacesEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: util_file_exists  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStream4nextEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLTokenC1ERK9XMLTripleRK13XMLAttributesjj    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK4List3getEj   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream14writeAttributeERKSsS1_S1_   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN16OutputCompressor16openBzip2OStreamERKSs  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStream8skipTextEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStreamC1ERSoRKSsbS2_S2_ (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK11XMLErrorLog12getNumErrorsEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes8readIntoERKSsRSsP11XMLErrorLogbjj (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNode8getChildEj    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLError17stringForCategoryEj    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStream11getEncodingEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken8isEndForERKS_   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLErrorC1EiRKSsjjjj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces6getURIEi  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken9getColumnEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLTokenD1Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces16getIndexByPrefixESs  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLAttributes8readIntoERKSsRiP11XMLErrorLogbjj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream10endElementERKSsS1_  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLNamespacesC1Ev    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeaSERKS_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeC1ER14XMLInputStream   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken6getURIEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker22hasExpectedXHTMLSyntaxEPK7XMLNodeP14SBMLNamespaces    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK13XMLNamespaces9getPrefixERKSs    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken13getAttributesEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream12startElementERKSsS1_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN4List3addEPv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN7XMLNodeC1ERKS_    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN11XMLErrorLogD2Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN16OutputCompressor14openZipOStreamERKSsS1_ (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken7isStartEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStream11skipPastEndERK8XMLToken  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN14XMLInputStream4peekEv    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLErrorC2ERKS_   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN11XMLErrorLogC2Ev  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK7XMLNode8getChildEj   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLNamespacesD1Ev    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN19RDFAnnotationParser16hasRDFAnnotationEPK7XMLNode (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13SyntaxChecker14checkAndSetSIdERKSsRSs    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLErrorC2EiRKSsjjjj  (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN13XMLNamespaces6removeEi   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: strcmp_insensitive    (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN8XMLToken8unsetEndEv   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken9getPrefixEv (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZN15XMLOutputStream14writeAttributeERKSsS1_RKd   (/usr/lib64/libsedml.so.0.3.0)
undefined symbol: _ZNK8XMLToken15getNamespaceURIERKSs   (/usr/lib64/libsedml.so.0.3.0)

cmake is set in this way:

export LDFLAGS="%{__global_ldflags} -Wl,--as-needed"
##Fix 'some warnings being treated as errors'
##https://github.com/fbergmann/libSEDML/issues/8
SEDMLOPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-Werror=format-security/-Wno-error=unused-value/g')
export CFLAGS="$SEDMLOPT_FLAGS"
export CXXFLAGS="$SEDMLOPT_FLAGS"
%cmake -Wno-dev \
%if 0%{?with_python2}
 -DWITH_PYTHON:BOOL=ON \
 -DWITH_SWIG:BOOL=ON \
 -DPYTHON_EXECUTABLE:FILEPATH=%{__python2} \
 -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python2_version} \
 -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python2_version}.so \
%endif
%if 0%{?with_java}
 -DWITH_JAVA:BOOL=ON \
 -DWITH_SWIG:BOOL=ON \
%endif
%if 0%{?with_octave}
 -DWITH_OCTAVE:BOOL=ON \
%endif
%if 0%{?with_perl}
 -DWITH_PERL:BOOL=ON \
%endif
%if 0%{?with_ruby}
 -DWITH_RUBY:BOOL=ON \
%endif
%if 0%{?with_r}
 -DWITH_R:BOOL=ON \
 -DR_INCLUDE_DIRS:PATH=%{_includedir}/R \
%endif
%if 0%{?with_mono}
 -DWITH_CSHARP:BOOL=ON \
 -DWITH_SWIG:BOOL=ON \
%if 0%{?fedora} > 22
 -DCSHARP_COMPILER:FILEPATH=%{_bindir}/mcs \
%endif
%endif
%if 0%{?with_doc}
 -DWITH_DOXYGEN:BOOL=ON \
%endif
%if 0%{?with_check}
 -DWITH_CHECK:BOOL=ON \
 -DWITH_EXAMPLES:BOOL=ON \
%endif
 -DCMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING="-L%{_libdir} -lxml2 -lz -lbz2 -lpthread" \
 -DLIBSBML_LIBRARY=%{_libdir} -DLIBSBML_INCLUDE_DIR:PATH=%{_includedir} \
 -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_INSTALL_LIBDIR:PATH=%{_libdir} \
 -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} -DLIBSEDML_SHARED_VERSION:BOOL=ON \
 -DEXTRA_LIBS:STRING="xml2;bz2;z" -DLIBSBML_STATIC:BOOL=OFF \
 -DCMAKE_CXX_FLAGS_RELEASE:STRING=" -I%{_includedir}/libxml2" \
 -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_COLOR_MAKEFILE:BOOL=ON \
 -DCPACK_BINARY_TZ:BOOL=OFF -DCPACK_BINARY_TGZ:BOOL=OFF \
 -DCPACK_SOURCE_TBZ2:BOOL=OFF -DCPACK_SOURCE_TGZ:BOOL=OFF \
 -DCPACK_SOURCE_TZ:BOOL=OFF -DWITH_ZLIB:BOOL=ON -DWITH_CPP_NAMESPACE:BOOL=OFF \
 -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES ..

Build fails (does not use correct libSBML path) on Mac OS X

The build system appears to be looking for -lsbml when linking instead of the absolute path to the library. Also, I'm passing -DLIBSBML_STATIC=ON but CMake doesn't appear to be picking up on it.

Here is my command line. I'm also setting CMAKE_PREFIX_PATH to include /path/to/libsbml/lib/cmake (not shown).

cmake -G"Xcode" -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_INSTALL_PREFIX=/Users/phantom/devel/install/libsedml-osx-10.9 -DLIBSBML_LIBRARY=/Users/phantom/devel/install/libsbml-experimental-osx-10.9/lib/libsbml-static.a -DLIBSBML_INCLUDE_DIR=/Users/phantom/devel/install/libsbml-experimental-osx-10.9/include -DLIBSBML_STATIC=ON -DEXTRA_LIBS='xml2;bz2;z;iconv' -DWITH_PYTHON=OFF -DLIBNUML_LIBRARY=/Users/phantom/devel/install/libnuml-osx-10.9/lib/libnuml-static.a -DLIBNUML_INCLUDE_DIR=/Users/phantom/devel/install/libnuml-osx-10.9/include /Users/phantom/devel/src/libsedml

Here is an example linker error:

Ld /Users/phantom/devel/build/libsedml-osx-10.9/sedml/Release/libsedml.0.4.2.dylib normal x86_64
    cd /Users/phantom/devel/src/libsedml
    export MACOSX_DEPLOYMENT_TARGET=10.9
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++ -arch x86_64 -dynamiclib -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -L/Users/phantom/devel/build/libsedml-osx-10.9/sedml/Release -F/Users/phantom/devel/build/libsedml-osx-10.9/sedml/Release -filelist /Users/phantom/devel/build/libsedml-osx-10.9/sedml/libsedml.build/Release/sedml.build/Objects-normal/x86_64/sedml.0.4.2.LinkFileList -install_name /libsedml.0.4.2.dylib -mmacosx-version-min=10.9 -dynamiclib -Wl,-headerpad_max_install_names -install_name /Users/phantom/devel/build/libsedml-osx-10.9/sedml/Release/libsedml.0.dylib -lsbml -lnuml -lxml2 -lbz2 -lz -liconv -single_module -current_version 0.4.2 -Xlinker -dependency_info -Xlinker /Users/phantom/devel/build/libsedml-osx-10.9/sedml/libsedml.build/Release/sedml.build/Objects-normal/x86_64/sedml.0.4.2_dependency_info.dat -o /Users/phantom/devel/build/libsedml-osx-10.9/sedml/Release/libsedml.0.4.2.dylib
ld: library not found for -lsbml
clang: error: linker command failed with exit code 1 (use -v to see invocation)

I'm using libSBML experimental rev 23757 FWIW.

python 3.5 language bindings installed despite py 2.7 being default

Before when building libsedml with python bindings the python 2.7 version was installed, now suddenly the python 3.5 version is installed, despite 2.7 being the default system version

mkoenig@core1:~$ python --version
Python 2.7.12

-- Installing: /usr/local/lib/python3.5/site-packages/libsedml/_libsedml.so
-- Installing: /usr/local/lib/python3.5/site-packages/libsedml.pth
-- Installing: /usr/local/lib/python3.5/site-packages/libsedml/libsedml.py

libsedml should install the language bindings for the system version of python.

I could fix this by providing the following build option

-DPYTHON_EXECUTABLE="/usr/bin/python"

but by default the system version of python should be used.

[libSEDML 0.3.0] LIBSEDML_SEV_* errors

Hi all.

There are various errors when i try to build libSEDML on Fedora 21 x86_64; i don't know if they are related to libSBML libraries.

+ LDFLAGS='-Wl,-z,relro  -Wl,--as-needed'
+ export LDFLAGS
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DWITH_CHECK:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=Debug -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DCMAKE_INSTALL_PREFIX:PATH=/usr -DLIBSEDML_SHARED_VERSION:BOOL=ON -DLIBSBML_INCLUDE_DIR:PATH=/usr/include '-DEXTRA_LIBS:STRING=xml2;bz2;z;iconv' -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCPACK_BINARY_TZ:BOOL=OFF -DCPACK_BINARY_TGZ:BOOL=OFF -DCPACK_SOURCE_TBZ2:BOOL=OFF -DCPACK_SOURCE_TGZ:BOOL=OFF -DCPACK_SOURCE_TZ:BOOL=OFF -DWITH_ZLIB:BOOL=ON -DWITH_CPP_NAMESPACE:BOOL=ON -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES ..
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /usr/lib64/ccache/cc
-- Check for working C compiler: /usr/lib64/ccache/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/lib64/ccache/c++
-- Check for working CXX compiler: /usr/lib64/ccache/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working C compiler: /usr/lib64/ccache/cc -- works
-- Looking for gzopen in /usr/lib64/libz.so
-- Looking for gzopen in /usr/lib64/libz.so - found
-- Looking for include file check.h
-- Looking for include file check.h - found
-- Looking for include file expat.h
-- Looking for include file expat.h - found
-- Looking for include file errno.h
-- Looking for include file errno.h - found
-- Looking for include file ieeefp.h
-- Looking for include file ieeefp.h - not found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file float.h
-- Looking for include file float.h - found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- 
----------------------------------------------------------------------
libSEDML version 0.3.0
----------------------------------------------------------------------

   More information and the latest version are available online at
   https://github.com/fbergmann/libSEDML/

   Please report problems using the issue tracker at
   https://github.com/fbergmann/libSEDML/issues

   To contact the developers directly, email [email protected]

   Configured on host  
     host type                     = Linux
     host operating system         = Linux 3.17.7-300.fc21.x86_64
     host CPU architecture         = x86_64

   General build flags:
     CC                            = /usr/lib64/ccache/cc
     CXX                           = /usr/lib64/ccache/c++
     CPPFLAGS                      =  -DLINUX -DPACKAGE_VERSION="0.3.0"  -DPACKAGE_NAME="libsedml"
     CFLAGS                        = -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -fno-strict-aliasing -fPIC
     CXXFLAGS                      = -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -fno-strict-aliasing -fPIC
     LDFLAGS                       =  -Wl,-z,relro  -Wl,--as-needed

   SBML library configuration:
     SBML library                  = /usr/lib64/libsbml.so
     SBML include                  = -I/usr/include

  Other libSEDML configuration settings:
     Installation $prefix          = /usr
--   Value of $LD_LIBRARY_PATH     = 
--   Using SWIG                    = /usr/bin/swig
--   Using libcheck                = /usr/lib64/libcheck.so
-- 

--   Using C++ namespace for libSEDML (libsedml) = yes
-- 
----------------------------------------------------------------------
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_CXX_FLAGS_RELEASE
    CMAKE_C_FLAGS_RELEASE
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build
+ make
/usr/bin/cmake -H/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0 -B/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/CMakeFiles /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build'
make -f sedml/CMakeFiles/sedml.dir/build.make sedml/CMakeFiles/sedml.dir/depend
make[2]: Entering directory '/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build'
cd /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0 /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/sedml /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/sedml/CMakeFiles/sedml.dir/DependInfo.cmake --color=
Scanning dependencies of target sedml
make[2]: Leaving directory '/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build'
make -f sedml/CMakeFiles/sedml.dir/build.make sedml/CMakeFiles/sedml.dir/build
make[2]: Entering directory '/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build'
/usr/bin/cmake -E cmake_progress_report /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/CMakeFiles 1
[  1%] Building CXX object sedml/CMakeFiles/sedml.dir/common/libsedml-version.cpp.o
cd /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/sedml && /usr/lib64/ccache/c++   -DLIBSEDML_EXPORTS=1 -DLIBSEDML_USE_CPP_NAMESPACE -DLINUX -DPACKAGE_NAME=\"libsedml\" -DPACKAGE_VERSION=\"0.3.0\" -DUSE_ZLIB -Dsedml_EXPORTS -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -fno-strict-aliasing -fPIC -g -fPIC -I/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/sedml/.. -I/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/.. -I/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml    -o CMakeFiles/sedml.dir/common/libsedml-version.cpp.o -c /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/common/libsedml-version.cpp
/usr/bin/cmake -E cmake_progress_report /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/CMakeFiles 2
[  2%] Building CXX object sedml/CMakeFiles/sedml.dir/SedFunctionalRange.cpp.o
cd /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/sedml && /usr/lib64/ccache/c++   -DLIBSEDML_EXPORTS=1 -DLIBSEDML_USE_CPP_NAMESPACE -DLINUX -DPACKAGE_NAME=\"libsedml\" -DPACKAGE_VERSION=\"0.3.0\" -DUSE_ZLIB -Dsedml_EXPORTS -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -fno-strict-aliasing -fPIC -g -fPIC -I/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/build/sedml/.. -I/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/.. -I/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml    -o CMakeFiles/sedml.dir/SedFunctionalRange.cpp.o -c /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:203:16: error: 'List' does not name a type
   static const List* getSupportedNamespaces();
                ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:261:3: error: 'XMLNamespaces' does not name a type
   XMLNamespaces * getNamespaces();
   ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:277:9: error: 'XMLNamespaces' does not name a type
   const XMLNamespaces * getNamespaces() const;
         ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:393:27: error: 'XMLNamespaces' does not name a type
   int addNamespaces(const XMLNamespaces * xmlns);
                           ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:464:22: error: 'XMLNamespaces' has not been declared
   void setNamespaces(XMLNamespaces * xmlns);
                      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:475:3: error: 'XMLNamespaces' does not name a type
   XMLNamespaces * mNamespaces;
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:510:1: error: 'XMLNamespaces_t' does not name a type
 XMLNamespaces_t *
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:522:36: error: 'XMLNamespaces_t' does not name a type
                              const XMLNamespaces_t * xmlns);
                                    ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedErrorLog.h:83:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:153,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:937:23: error: 'LIBSBML_SEV_ERROR' was not declared in this scope
  LIBSEDML_SEV_ERROR = LIBSBML_SEV_ERROR,
                       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:937:23: note: suggested alternative:
In file included from /usr/include/sbml/SBase.h:154:0,
                 from /usr/include/sbml/SyntaxChecker.h:49,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:141,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/xml/XMLError.h:525:5: note:   'LIBSBML_SEV_ERROR'
   , LIBSBML_SEV_ERROR       /*!< The error object represents a serious error.  The
     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedErrorLog.h:83:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:153,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:938:23: error: 'LIBSBML_SEV_FATAL' was not declared in this scope
  LIBSEDML_SEV_FATAL = LIBSBML_SEV_FATAL,
                       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:938:23: note: suggested alternative:
In file included from /usr/include/sbml/SBase.h:154:0,
                 from /usr/include/sbml/SyntaxChecker.h:49,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:141,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/xml/XMLError.h:530:5: note:   'LIBSBML_SEV_FATAL'
   , LIBSBML_SEV_FATAL       /*!< A serious error occurred, such as an
     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedErrorLog.h:83:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:153,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:939:25: error: 'LIBSBML_SEV_WARNING' was not declared in this scope
  LIBSEDML_SEV_WARNING = LIBSBML_SEV_WARNING,
                         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:939:25: note: suggested alternative:
In file included from /usr/include/sbml/SBase.h:154:0,
                 from /usr/include/sbml/SyntaxChecker.h:49,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:141,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/xml/XMLError.h:520:5: note:   'LIBSBML_SEV_WARNING'
   , LIBSBML_SEV_WARNING     /*!< The error object represents a problem that is not
     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedErrorLog.h:83:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:153,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:941:34: error: 'LIBSBML_SEV_FATAL' was not declared in this scope
     LIBSEDML_SEV_SCHEMA_ERROR    = (LIBSBML_SEV_FATAL + 1)
                                  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:941:34: note: suggested alternative:
In file included from /usr/include/sbml/SBase.h:154:0,
                 from /usr/include/sbml/SyntaxChecker.h:49,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:141,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/xml/XMLError.h:530:5: note:   'LIBSBML_SEV_FATAL'
   , LIBSBML_SEV_FATAL       /*!< A serious error occurred, such as an
     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedErrorLog.h:83:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:153,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedError.h:970:1: error: expected class-name before '{' token
 {
 ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:153:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedErrorLog.h:93:1: error: expected class-name before '{' token
 {
 ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:2387:38: error: 'ExpectedAttributes' has not been declared
   virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:2395:38: error: 'ExpectedAttributes' does not name a type
                                const ExpectedAttributes& expectedAttributes);
                                      ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:2698:39: error: 'XMLNamespaces_t' has not been declared
 SedBase_setNamespaces (SedBase_t *sb, XMLNamespaces_t *xmlns);
                                       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:2788:7: error: 'Model_t' does not name a type
 const Model_t *
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:2834:1: error: 'List_t' does not name a type
 List_t* 
 ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:520:38: error: 'ExpectedAttributes' has not been declared
   virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:529:38: error: 'ExpectedAttributes' does not name a type
                                const ExpectedAttributes& expectedAttributes);
                                      ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:59:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRange.h:266:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:59:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRange.h:278:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:60:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedVariable.h:501:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:60:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedVariable.h:513:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:61:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedParameter.h:362:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:61:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedParameter.h:374:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:64:35: error: invalid use of incomplete type 'class libsedml::SedRange'
 class LIBSEDML_EXTERN SedFunctionalRange : public SedRange
                                   ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:136:15: error: forward declaration of 'class libsedml::SedRange'
 typedef CLASS_OR_STRUCT SedRange                     SedRange_t;
               ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:69:2: error: 'SedListOfVariables' does not name a type
  SedListOfVariables   mVariables;
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:70:2: error: 'SedListOfParameters' does not name a type
  SedListOfParameters   mParameters;
  ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:226:8: error: 'SedListOfVariables' does not name a type
  const SedListOfVariables* getListOfVariables() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:357:8: error: 'SedListOfParameters' does not name a type
  const SedListOfParameters* getListOfParameters() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:614:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:626:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:703:30: error: invalid covariant return type for 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(unsigned int)'
  virtual SedFunctionalRange* get(unsigned int n);
                              ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:268:20: error:   overriding 'virtual libsedml::SedBase* libsedml::SedListOf::get(unsigned int)'
   virtual SedBase* get (unsigned int n);
                    ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:715:36: error: invalid covariant return type for 'virtual const libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(unsigned int) const'
  virtual const SedFunctionalRange* get(unsigned int n) const;
                                    ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:256:26: error:   overriding 'virtual const libsedml::SedBase* libsedml::SedListOf::get(unsigned int) const'
   virtual const SedBase* get (unsigned int n) const;
                          ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:0:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:796:30: error: invalid covariant return type for 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::remove(unsigned int)'
  virtual SedFunctionalRange* remove(unsigned int n);
                              ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:370:20: error:   overriding 'virtual libsedml::SedBase* libsedml::SedListOf::remove(unsigned int)'
   virtual SedBase* remove (unsigned int n);
                    ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:46:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedChange.h:266:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:46:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedChange.h:278:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:47:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedChangeAttribute.h:278:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:47:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedChangeAttribute.h:290:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:48:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAddXML.h:278:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:48:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAddXML.h:290:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:49:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedChangeXML.h:278:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:49:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedChangeXML.h:290:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:50:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRemoveXML.h:230:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:50:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRemoveXML.h:242:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedComputeChange.h:69:2: error: 'SedListOfVariables' does not name a type
  SedListOfVariables   mVariables;
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedComputeChange.h:70:2: error: 'SedListOfParameters' does not name a type
  SedListOfParameters   mParameters;
  ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedComputeChange.h:179:8: error: 'SedListOfVariables' does not name a type
  const SedListOfVariables* getListOfVariables() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedComputeChange.h:310:8: error: 'SedListOfParameters' does not name a type
  const SedListOfParameters* getListOfParameters() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedComputeChange.h:566:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedComputeChange.h:578:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedModel.h:619:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedModel.h:631:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithm.h:59:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:53,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithmParameter.h:314:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithm.h:59:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:53,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithmParameter.h:326:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:53:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithm.h:67:2: error: 'SedListOfAlgorithmParameters' does not name a type
  SedListOfAlgorithmParameters   mAlgorithmParameters;
  ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:53:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithm.h:176:8: error: 'SedListOfAlgorithmParameters' does not name a type
  const SedListOfAlgorithmParameters* getListOfAlgorithmParameters() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:53:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithm.h:433:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:53:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedAlgorithm.h:445:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:55:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSimulation.h:402:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:55:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSimulation.h:414:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:56:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedUniformTimeCourse.h:426:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:56:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedUniformTimeCourse.h:438:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:57:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedOneStep.h:279:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:57:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedOneStep.h:291:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:58:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSteadyState.h:230:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:58:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSteadyState.h:242:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:59:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataSet.h:409:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:59:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataSet.h:421:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:60:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedCurve.h:506:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:60:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedCurve.h:518:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:61:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSurface.h:327:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:61:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSurface.h:339:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:62:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedOutput.h:347:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:62:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedOutput.h:359:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:63:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedReport.h:386:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:63:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedReport.h:398:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:64:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedPlot2D.h:386:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:64:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedPlot2D.h:398:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:65:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedPlot3D.h:386:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:65:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedPlot3D.h:398:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:66:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataGenerator.h:70:2: error: 'SedListOfVariables' does not name a type
  SedListOfVariables   mVariables;
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataGenerator.h:71:2: error: 'SedListOfParameters' does not name a type
  SedListOfParameters   mParameters;
  ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:66:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataGenerator.h:272:8: error: 'SedListOfVariables' does not name a type
  const SedListOfVariables* getListOfVariables() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:66:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataGenerator.h:403:8: error: 'SedListOfParameters' does not name a type
  const SedListOfParameters* getListOfParameters() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:66:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataGenerator.h:660:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:66:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDataGenerator.h:672:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:67:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTask.h:441:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:67:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTask.h:453:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:61:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSetValue.h:754:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:61:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSetValue.h:766:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:62:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSubTask.h:315:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:62:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedSubTask.h:327:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:73:2: error: 'SedListOfRanges' does not name a type
  SedListOfRanges   mRanges;
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:74:2: error: 'SedListOfTaskChanges' does not name a type
  SedListOfTaskChanges   mTaskChanges;
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:75:2: error: 'SedListOfSubTasks' does not name a type
  SedListOfSubTasks   mSubTasks;
  ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:229:8: error: 'SedListOfRanges' does not name a type
  const SedListOfRanges* getListOfRanges() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:382:8: error: 'SedListOfTaskChanges' does not name a type
  const SedListOfTaskChanges* getListOfTaskChanges() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:513:8: error: 'SedListOfSubTasks' does not name a type
  const SedListOfSubTasks* getListOfSubTasks() const;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:769:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:68:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedRepeatedTask.h:781:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:72:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedUniformRange.h:62:32: error: invalid use of incomplete type 'class libsedml::SedRange'
 class LIBSEDML_EXTERN SedUniformRange : public SedRange
                                ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:136:15: error: forward declaration of 'class libsedml::SedRange'
 typedef CLASS_OR_STRUCT SedRange                     SedRange_t;
               ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:72:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedUniformRange.h:425:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:72:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedUniformRange.h:437:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:73:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedVectorRange.h:62:31: error: invalid use of incomplete type 'class libsedml::SedRange'
 class LIBSEDML_EXTERN SedVectorRange : public SedRange
                               ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:136:15: error: forward declaration of 'class libsedml::SedRange'
 typedef CLASS_OR_STRUCT SedRange                     SedRange_t;
               ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:73:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedVectorRange.h:309:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:73:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedVectorRange.h:321:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:75:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDocument.h:1070:37: error: 'ExpectedAttributes' has not been declared
  virtual void addExpectedAttributes(ExpectedAttributes& attributes);
                                     ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:75:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedDocument.h:1082:37: error: 'ExpectedAttributes' does not name a type
                               const ExpectedAttributes& expectedAttributes);
                                     ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In constructor 'libsedml::SedFunctionalRange::SedFunctionalRange(unsigned int, unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:54:4: error: type 'libsedml::SedRange' is not a direct base of 'libsedml::SedFunctionalRange'
  : SedRange(level, version)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:55:4: error: class 'libsedml::SedFunctionalRange' does not have any field named 'mVariables'
  , mVariables (level, version)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:56:4: error: class 'libsedml::SedFunctionalRange' does not have any field named 'mParameters'
  , mParameters (level, version)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:62:58: error: 'setSedNamespacesAndOwn' was not declared in this scope
  setSedNamespacesAndOwn(new SedNamespaces(level, version));
                                                          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In constructor 'libsedml::SedFunctionalRange::SedFunctionalRange(libsedml::SedNamespaces*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:73:4: error: type 'libsedml::SedRange' is not a direct base of 'libsedml::SedFunctionalRange'
  : SedRange(sedns)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:74:4: error: class 'libsedml::SedFunctionalRange' does not have any field named 'mVariables'
  , mVariables (sedns)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:75:4: error: class 'libsedml::SedFunctionalRange' does not have any field named 'mParameters'
  , mParameters (sedns)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:81:37: error: 'setElementNamespace' was not declared in this scope
  setElementNamespace(sedns->getURI());
                                     ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In copy constructor 'libsedml::SedFunctionalRange::SedFunctionalRange(const libsedml::SedFunctionalRange&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:92:4: error: type 'libsedml::SedRange' is not a direct base of 'libsedml::SedFunctionalRange'
  : SedRange(orig)
    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:100:3: error: 'mVariables' was not declared in this scope
   mVariables  = orig.mVariables;
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:100:21: error: 'const class libsedml::SedFunctionalRange' has no member named 'mVariables'
   mVariables  = orig.mVariables;
                     ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:101:3: error: 'mParameters' was not declared in this scope
   mParameters  = orig.mParameters;
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:101:22: error: 'const class libsedml::SedFunctionalRange' has no member named 'mParameters'
   mParameters  = orig.mParameters;
                      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:103:44: error: invalid use of incomplete type 'class libsedml::ASTNode'
   mMath  = orig.mMath != NULL ? orig.mMath->deepCopy() : NULL;
                                            ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: error: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedFunctionalRange& libsedml::SedFunctionalRange::operator=(const libsedml::SedFunctionalRange&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:123:3: error: incomplete type 'libsedml::SedRange' used in nested name specifier
   SedRange::operator=(rhs);
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:124:3: error: 'mVariables' was not declared in this scope
   mVariables  = rhs.mVariables;
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:124:20: error: 'const class libsedml::SedFunctionalRange' has no member named 'mVariables'
   mVariables  = rhs.mVariables;
                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:125:3: error: 'mParameters' was not declared in this scope
   mParameters  = rhs.mParameters;
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:125:21: error: 'const class libsedml::SedFunctionalRange' has no member named 'mParameters'
   mParameters  = rhs.mParameters;
                     ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:127:42: error: invalid use of incomplete type 'class libsedml::ASTNode'
   mMath  = rhs.mMath != NULL ? rhs.mMath->deepCopy() : NULL;
                                          ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: error: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual int libsedml::SedFunctionalRange::setRange(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:204:13: error: 'SyntaxChecker' has not been declared
  else if (!(SyntaxChecker::isValidInternalSId(range)))
             ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual int libsedml::SedFunctionalRange::setMath(libsedml::ASTNode*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:228:10: warning: possible problem detected in invocation of delete operator: [-Wdelete-incomplete]
   delete mMath;
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:228:10: warning: invalid use of incomplete type 'class libsedml::ASTNode'
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: warning: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:228:10: note: neither the destructor nor the class-specific operator delete will be called, even if they are declared when the class is defined
   delete mMath;
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:232:17: error: invalid use of incomplete type 'class libsedml::ASTNode'
  else if (!(math->isWellFormedASTNode()))
                 ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: error: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:238:10: warning: possible problem detected in invocation of delete operator: [-Wdelete-incomplete]
   delete mMath;
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:238:10: warning: invalid use of incomplete type 'class libsedml::ASTNode'
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: warning: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:238:10: note: neither the destructor nor the class-specific operator delete will be called, even if they are declared when the class is defined
   delete mMath;
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:240:8: error: invalid use of incomplete type 'class libsedml::ASTNode'
    math->deepCopy() : NULL;
        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: error: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual int libsedml::SedFunctionalRange::unsetMath()':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:274:9: warning: possible problem detected in invocation of delete operator: [-Wdelete-incomplete]
  delete mMath;
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:274:9: warning: invalid use of incomplete type 'class libsedml::ASTNode'
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: warning: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:274:9: note: neither the destructor nor the class-specific operator delete will be called, even if they are declared when the class is defined
  delete mMath;
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: At global scope:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:283:7: error: 'SedListOfVariables' does not name a type
 const SedListOfVariables*
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::removeVariable(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:296:9: error: 'mVariables' was not declared in this scope
  return mVariables.remove(n);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::removeVariable(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:306:9: error: 'mVariables' was not declared in this scope
  return mVariables.remove(sid);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:316:9: error: 'mVariables' was not declared in this scope
  return mVariables.get(n);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(unsigned int) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:326:9: error: 'mVariables' was not declared in this scope
  return mVariables.get(n);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:336:9: error: 'mVariables' was not declared in this scope
  return mVariables.get(sid);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(const string&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:346:9: error: 'mVariables' was not declared in this scope
  return mVariables.get(sid);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'int libsedml::SedFunctionalRange::addVariable(const libsedml::SedVariable*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:366:2: error: 'mVariables' was not declared in this scope
  mVariables.append(sv);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'unsigned int libsedml::SedFunctionalRange::getNumVariables() const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:379:9: error: 'mVariables' was not declared in this scope
  return mVariables.size();
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::createVariable()':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:393:38: error: invalid use of incomplete type 'class libsedml::SedVariable'
  SedVariable *temp = new SedVariable();
                                      ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:117:15: error: forward declaration of 'class libsedml::SedVariable'
 typedef CLASS_OR_STRUCT SedVariable                     SedVariable_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:394:22: error: 'mVariables' was not declared in this scope
  if (temp != NULL) mVariables.appendAndOwn(temp);
                      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: At global scope:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:401:7: error: 'SedListOfParameters' does not name a type
 const SedListOfParameters*
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::removeParameter(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:414:9: error: 'mParameters' was not declared in this scope
  return mParameters.remove(n);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::removeParameter(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:424:9: error: 'mParameters' was not declared in this scope
  return mParameters.remove(sid);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:434:9: error: 'mParameters' was not declared in this scope
  return mParameters.get(n);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(unsigned int) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:444:9: error: 'mParameters' was not declared in this scope
  return mParameters.get(n);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:454:9: error: 'mParameters' was not declared in this scope
  return mParameters.get(sid);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(const string&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:464:9: error: 'mParameters' was not declared in this scope
  return mParameters.get(sid);
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'int libsedml::SedFunctionalRange::addParameter(const libsedml::SedParameter*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:484:2: error: 'mParameters' was not declared in this scope
  mParameters.append(sp);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'unsigned int libsedml::SedFunctionalRange::getNumParameters() const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:497:9: error: 'mParameters' was not declared in this scope
  return mParameters.size();
         ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::createParameter()':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:511:40: error: invalid use of incomplete type 'class libsedml::SedParameter'
  SedParameter *temp = new SedParameter();
                                        ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:123:15: error: forward declaration of 'class libsedml::SedParameter'
 typedef CLASS_OR_STRUCT SedParameter                     SedParameter_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:512:22: error: 'mParameters' was not declared in this scope
  if (temp != NULL) mParameters.appendAndOwn(temp);
                      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedBase* libsedml::SedFunctionalRange::createObject(libsedml::XMLInputStream&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:533:20: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  SedBase* object = SedRange::createObject(stream);
                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:535:29: error: invalid use of incomplete type 'class libsedml::XMLInputStream'
  const string& name   = stream.peek().getName();
                             ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:165:7: error: forward declaration of 'class libsedml::XMLInputStream'
 class XMLInputStream;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:539:13: error: 'mVariables' was not declared in this scope
   object = &mVariables;
             ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:544:13: error: 'mParameters' was not declared in this scope
   object = &mParameters;
             ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual void libsedml::SedFunctionalRange::connectToChild()':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:559:2: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  SedRange::connectToChild();
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:561:2: error: 'mVariables' was not declared in this scope
  mVariables.connectToParent(this);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:562:2: error: 'mParameters' was not declared in this scope
  mParameters.connectToParent(this);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual bool libsedml::SedFunctionalRange::hasRequiredAttributes() const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:582:20: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  bool allPresent = SedRange::hasRequiredAttributes();
                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual bool libsedml::SedFunctionalRange::hasRequiredElements() const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:597:20: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  bool allPresent = SedRange::hasRequiredElements();
                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual void libsedml::SedFunctionalRange::writeElements(libsedml::XMLOutputStream&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:611:2: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  SedRange::writeElements(stream);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:614:3: error: 'mVariables' was not declared in this scope
   mVariables.write(stream);
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:618:3: error: 'mParameters' was not declared in this scope
   mParameters.write(stream);
   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:622:40: error: 'writeMathML' was not declared in this scope
   writeMathML(getMath(), stream, NULL);
                                        ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:622:40: note: suggested alternative:
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:86:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/usr/include/sbml/math/MathML.h:78:1: note:   'libsbml::writeMathML'
 writeMathML (const ASTNode* node, XMLOutputStream& stream, SBMLNamespaces *sbmlns=NULL);
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual void libsedml::SedFunctionalRange::setSedDocument(libsedml::SedDocument*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:654:2: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  SedRange::setSedDocument(d);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:655:2: error: 'mVariables' was not declared in this scope
  mVariables.setSedDocument(d);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:656:2: error: 'mParameters' was not declared in this scope
  mParameters.setSedDocument(d);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: At global scope:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:669:43: error: variable or field 'addExpectedAttributes' declared void
 SedFunctionalRange::addExpectedAttributes(ExpectedAttributes& attributes)
                                           ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:669:43: error: 'ExpectedAttributes' was not declared in this scope
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:669:43: note: suggested alternative:
In file included from /usr/include/sbml/SBase.h:152:0,
                 from /usr/include/sbml/SyntaxChecker.h:49,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:141,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/ExpectedAttributes.h:51:7: note:   'libsbml::ExpectedAttributes'
 class LIBSBML_EXTERN ExpectedAttributes
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:669:63: error: 'attributes' was not declared in this scope
 SedFunctionalRange::addExpectedAttributes(ExpectedAttributes& attributes)
                                                               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:687:36: error: 'ExpectedAttributes' does not name a type
                              const ExpectedAttributes& expectedAttributes)
                                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual void libsedml::SedFunctionalRange::readAttributes(const libsedml::XMLAttributes&, const int&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:689:2: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  SedRange::readAttributes(attributes, expectedAttributes);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:696:23: error: invalid use of incomplete type 'const class libsedml::XMLAttributes'
  assigned = attributes.readInto("range", mRange, getErrorLog(), true);
                       ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:164:7: error: forward declaration of 'const class libsedml::XMLAttributes'
 class XMLAttributes;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:696:62: error: 'getErrorLog' was not declared in this scope
  assigned = attributes.readInto("range", mRange, getErrorLog(), true);
                                                              ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:704:36: error: 'getLevel' was not declared in this scope
    logEmptyString(mRange, getLevel(), getVersion(), "<SedFunctionalRange>");
                                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:704:50: error: 'getVersion' was not declared in this scope
    logEmptyString(mRange, getLevel(), getVersion(), "<SedFunctionalRange>");
                                                  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:704:75: error: 'logEmptyString' was not declared in this scope
    logEmptyString(mRange, getLevel(), getVersion(), "<SedFunctionalRange>");
                                                                           ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:706:12: error: 'SyntaxChecker' has not been declared
   else if (SyntaxChecker::isValidSBMLSId(mRange) == false)
            ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:708:31: error: 'logError' was not declared in this scope
    logError(SedInvalidIdSyntax);
                               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual bool libsedml::SedFunctionalRange::readOtherXML(libsedml::XMLInputStream&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:724:29: error: invalid use of incomplete type 'class libsedml::XMLInputStream'
  const string& name = stream.peek().getName();
                             ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:165:7: error: forward declaration of 'class libsedml::XMLInputStream'
 class XMLInputStream;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:728:18: error: variable 'const libsedml::XMLToken elem' has initializer but incomplete type
   const XMLToken elem = stream.peek();
                  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:728:31: error: invalid use of incomplete type 'class libsedml::XMLInputStream'
   const XMLToken elem = stream.peek();
                               ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:165:7: error: forward declaration of 'class libsedml::XMLInputStream'
 class XMLInputStream;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:729:55: error: 'checkMathMLNamespace' was not declared in this scope
   const std::string prefix = checkMathMLNamespace(elem);
                                                       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:731:10: warning: possible problem detected in invocation of delete operator: [-Wdelete-incomplete]
   delete mMath;
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:731:10: warning: invalid use of incomplete type 'class libsedml::ASTNode'
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:42:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/sedmlfwd.h:334:15: warning: forward declaration of 'class libsedml::ASTNode'
 typedef CLASS_OR_STRUCT ASTNode                     ASTNode_t;
               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:731:10: note: neither the destructor nor the class-specific operator delete will be called, even if they are declared when the class is defined
   delete mMath;
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:732:36: error: 'readMathML' was not declared in this scope
   mMath = readMathML(stream, prefix);
                                    ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:732:36: note: suggested alternative:
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedTypes.h:86:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:38:
/usr/include/sbml/math/MathML.h:67:1: note:   'libsbml::readMathML'
 readMathML (XMLInputStream& stream, const std::string& reqd_prefix="");
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:736:6: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  if (SedRange::readOtherXML(stream))
      ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual void libsedml::SedFunctionalRange::writeAttributes(libsedml::XMLOutputStream&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:755:2: error: incomplete type 'libsedml::SedRange' used in nested name specifier
  SedRange::writeAttributes(stream);
  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:758:9: error: invalid use of incomplete type 'class libsedml::XMLOutputStream'
   stream.writeAttribute("range", getPrefix(), mRange);
         ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:167:7: error: forward declaration of 'class libsedml::XMLOutputStream'
 class XMLOutputStream;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:758:44: error: 'getPrefix' was not declared in this scope
   stream.writeAttribute("range", getPrefix(), mRange);
                                            ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:803:59: error: invalid static_cast from type 'libsedml::SedBase*' to type 'libsedml::SedFunctionalRange*'
  return static_cast<SedFunctionalRange*>(SedListOf::get(n));
                                                           ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual const libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(unsigned int) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:813:65: error: invalid static_cast from type 'const libsedml::SedBase*' to type 'const libsedml::SedFunctionalRange*'
  return static_cast<const SedFunctionalRange*>(SedListOf::get(n));
                                                                 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual const libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(const string&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:837:82: error: invalid static_cast from type 'libsedml::SedBase* const' to type 'libsedml::SedFunctionalRange*'
  return (result == mItems.end()) ? 0 : static_cast <SedFunctionalRange*> (*result);
                                                                                  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'int libsedml::SedListOfFunctionalRanges::addFunctionalRange(const libsedml::SedFunctionalRange*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:857:12: error: no matching function for call to 'libsedml::SedListOfFunctionalRanges::append(const libsedml::SedFunctionalRange*&)'
  append(sfr);
            ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:857:12: note: candidate is:
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:190:7: note: int libsedml::SedListOf::append(const libsedml::SedBase*)
   int append (const SedBase* item);
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:190:7: note:   no known conversion for argument 1 from 'const libsedml::SedFunctionalRange*' to 'const libsedml::SedBase*'
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::createFunctionalRange()':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:885:39: error: no matching function for call to 'libsedml::SedListOfFunctionalRanges::appendAndOwn(libsedml::SedFunctionalRange*&)'
  if (temp != NULL) appendAndOwn(temp);
                                       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:885:39: note: candidate is:
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:204:7: note: int libsedml::SedListOf::appendAndOwn(libsedml::SedBase*)
   int appendAndOwn (SedBase* item);
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:204:7: note:   no known conversion for argument 1 from 'libsedml::SedFunctionalRange*' to 'libsedml::SedBase*'
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::remove(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:895:62: error: invalid static_cast from type 'libsedml::SedBase*' to type 'libsedml::SedFunctionalRange*'
  return static_cast<SedFunctionalRange*>(SedListOf::remove(n));
                                                              ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::remove(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:916:48: error: invalid static_cast from type 'libsedml::SedBase*' to type 'libsedml::SedFunctionalRange*'
  return static_cast <SedFunctionalRange*> (item);
                                                ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedBase* libsedml::SedListOfFunctionalRanges::createObject(libsedml::XMLInputStream&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:959:34: error: invalid use of incomplete type 'class libsedml::XMLInputStream'
  const std::string& name   = stream.peek().getName();
                                  ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:165:7: error: forward declaration of 'class libsedml::XMLInputStream'
 class XMLInputStream;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:964:10: error: cannot convert 'libsedml::SedFunctionalRange*' to 'libsedml::SedBase*' in assignment
   object = new SedFunctionalRange(getSedNamespaces());
          ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual void libsedml::SedListOfFunctionalRanges::writeXMLNS(libsedml::XMLOutputStream&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:983:16: error: aggregate 'libsedml::XMLNamespaces xmlns' has incomplete type and cannot be defined
  XMLNamespaces xmlns;
                ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:989:52: error: invalid use of incomplete type 'class libsedml::XMLNamespaces'
   if (getNamespaces() != NULL && !getNamespaces()->hasURI(SEDML_XMLNS_L1) && !getNamespaces()->hasURI(SEDML_XMLNS_L1V2))
                                                    ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:166:7: error: forward declaration of 'class libsedml::XMLNamespaces'
 class XMLNamespaces;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:989:96: error: invalid use of incomplete type 'class libsedml::XMLNamespaces'
   if (getNamespaces() != NULL && !getNamespaces()->hasURI(SEDML_XMLNS_L1) && !getNamespaces()->hasURI(SEDML_XMLNS_L1V2))
                                                                                                ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:166:7: error: forward declaration of 'class libsedml::XMLNamespaces'
 class XMLNamespaces;
       ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'char* libsedml::SedFunctionalRange_getRange(libsedml::SedFunctionalRange_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1054:79: error: 'safe_strdup' was not declared in this scope
  return sfr->getRange().empty() ? NULL : safe_strdup(sfr->getRange().c_str());
                                                                               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1054:79: note: suggested alternative:
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/common/common.h:116:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:74,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/util/util.h:110:1: note:   'libsbml::safe_strdup'
 safe_strdup (const char* s);
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'int libsedml::SedFunctionalRange_addVariable(libsedml::SedFunctionalRange_t*, libsedml::SedVariable_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1142:50: error: 'LIBSBML_INVALID_OBJECT' was not declared in this scope
  return  (sfr != NULL) ? sfr->addVariable(sv) : LIBSBML_INVALID_OBJECT;
                                                  ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1142:50: note: suggested alternative:
In file included from /usr/include/sbml/xml/XMLNamespaces.h:65:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:73,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/common/operationReturnValues.h:87:5: note:   'LIBSBML_INVALID_OBJECT'
   , LIBSBML_INVALID_OBJECT          = -5
     ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'libsedml::SedListOf_t* libsedml::SedFunctionalRange_getSedListOfVariables(libsedml::SedFunctionalRange_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1156:47: error: 'libsedml::SedFunctionalRange_t' has no member named 'getListOfVariables'
  return  (sfr != NULL) ? (SedListOf_t *)sfr->getListOfVariables() : NULL;
                                               ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'int libsedml::SedFunctionalRange_addParameter(libsedml::SedFunctionalRange_t*, libsedml::SedParameter_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1198:51: error: 'LIBSBML_INVALID_OBJECT' was not declared in this scope
  return  (sfr != NULL) ? sfr->addParameter(sp) : LIBSBML_INVALID_OBJECT;
                                                   ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1198:51: note: suggested alternative:
In file included from /usr/include/sbml/xml/XMLNamespaces.h:65:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedNamespaces.h:73,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedBase.h:139,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:51,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/usr/include/sbml/common/operationReturnValues.h:87:5: note:   'LIBSBML_INVALID_OBJECT'
   , LIBSBML_INVALID_OBJECT          = -5
     ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'libsedml::SedListOf_t* libsedml::SedFunctionalRange_getSedListOfParameters(libsedml::SedFunctionalRange_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1212:47: error: 'libsedml::SedFunctionalRange_t' has no member named 'getListOfParameters'
  return  (sfr != NULL) ? (SedListOf_t *)sfr->getListOfParameters() : NULL;
                                               ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h: In instantiation of 'bool libsedml::SedIdEq<CNAME>::operator()(libsedml::SedBase*) [with CNAME = libsedml::SedFunctionalRange]':
/usr/include/c++/4.9.2/bits/predefined_ops.h:231:30:   required from 'bool __gnu_cxx::__ops::_Iter_pred<_Predicate>::operator()(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<libsedml::SedBase* const*, std::vector<libsedml::SedBase*> >; _Predicate = libsedml::SedIdEq<libsedml::SedFunctionalRange>]'
/usr/include/c++/4.9.2/bits/stl_algo.h:120:22:   required from '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<libsedml::SedBase* const*, std::vector<libsedml::SedBase*> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<libsedml::SedIdEq<libsedml::SedFunctionalRange> >]'
/usr/include/c++/4.9.2/bits/stl_algo.h:162:43:   required from '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator<libsedml::SedBase* const*, std::vector<libsedml::SedBase*> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<libsedml::SedIdEq<libsedml::SedFunctionalRange> >]'
/usr/include/c++/4.9.2/bits/stl_algo.h:3804:45:   required from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator<libsedml::SedBase* const*, std::vector<libsedml::SedBase*> >; _Predicate = libsedml::SedIdEq<libsedml::SedFunctionalRange>]'
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:836:83:   required from here
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:106:17: error: invalid static_cast from type 'libsedml::SedBase*' to type 'libsedml::SedFunctionalRange*'
        { return static_cast <CNAME*> (sb)->getId() == id; }
                 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual int libsedml::SedFunctionalRange::setRange(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:213:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual int libsedml::SedFunctionalRange::setMath(libsedml::ASTNode*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:246:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::removeVariable(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:297:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::removeVariable(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:307:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:317:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(unsigned int) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:327:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:337:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedVariable* libsedml::SedFunctionalRange::getVariable(const string&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:347:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'unsigned int libsedml::SedFunctionalRange::getNumVariables() const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:380:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::removeParameter(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:415:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::removeParameter(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:425:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:435:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(unsigned int) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:445:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:455:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'const libsedml::SedParameter* libsedml::SedFunctionalRange::getParameter(const string&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:465:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'unsigned int libsedml::SedFunctionalRange::getNumParameters() const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:498:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:804:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual const libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(unsigned int) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:814:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual const libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::get(const string&) const':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:838:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
In file included from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedFunctionalRange.h:52:0,
                 from /home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:37:
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h: In member function 'bool libsedml::SedIdEq<CNAME>::operator()(libsedml::SedBase*) [with CNAME = libsedml::SedFunctionalRange]':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/../sedml/SedListOf.h:106:59: warning: control reaches end of non-void function [-Wreturn-type]
        { return static_cast <CNAME*> (sb)->getId() == id; }
                                                           ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::remove(unsigned int)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:896:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In member function 'virtual libsedml::SedFunctionalRange* libsedml::SedListOfFunctionalRanges::remove(const string&)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:917:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'char* libsedml::SedFunctionalRange_getRange(libsedml::SedFunctionalRange_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1055:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'int libsedml::SedFunctionalRange_addVariable(libsedml::SedFunctionalRange_t*, libsedml::SedVariable_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1143:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'libsedml::SedListOf_t* libsedml::SedFunctionalRange_getSedListOfVariables(libsedml::SedFunctionalRange_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1157:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'int libsedml::SedFunctionalRange_addParameter(libsedml::SedFunctionalRange_t*, libsedml::SedParameter_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1199:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp: In function 'libsedml::SedListOf_t* libsedml::SedFunctionalRange_getSedListOfParameters(libsedml::SedFunctionalRange_t*)':
/home/sagitter/rpmbuild/BUILD/libSEDML-0.3.0/sedml/SedFunctionalRange.cpp:1213:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
sedml/CMakeFiles/sedml.dir/build.make:80: recipe for target 'sedml/CMakeFiles/sedml.dir/SedFunctionalRange.cpp.o' failed

Missing tests

Hello,

are tests defined during libsedml build?
-DWITH_CHECK option seems be useless.

libsbml on Ubuntu linux not found by cmake anymore

Hi all,
I just updated libsbml and libsedml on Ubuntu (both building from latest source), but with the latest changes the libsbml include dir cannot be found.
This was never a problem before.

libsbml is installing in the /usr/local/include/sbml folder.

Install the project...
-- Install configuration: "Release"
-- Installing: /usr/local/share/libsbml/./COPYING.txt
-- Installing: /usr/local/share/libsbml/./FUNDING.txt
-- Installing: /usr/local/share/libsbml/./LICENSE.txt
-- Installing: /usr/local/share/libsbml/./NEWS.txt
-- Installing: /usr/local/share/libsbml/./OLD_NEWS.txt
-- Installing: /usr/local/share/libsbml/./README.txt
-- Installing: /usr/local/share/libsbml/./VERSION.txt
-- Installing: /usr/local/lib/pkgconfig/libsbml.pc
-- Installing: /usr/local/include/sbml/packages/comp/common/CompExtensionTypes.h
-- Installing: /usr/local/include/sbml/packages/comp/common/compfwd.h
-- Installing: /usr/local/include/sbml/packages/comp/extension/CompExtension.h
-- Installing: /usr/local/include/sbml/packages/comp/extension/CompModelPlugin.h
...

When than trying to build libsedml I get

--------------------------------------
pull libSEDML repository
--------------------------------------
/home/mkoenig/git/libSEDML
From https://github.com/fbergmann/libSEDML
   ebd9e61..ee18e61  master     -> origin/master
Updating ebd9e61..ee18e61
Fast-forward
 CMakeLists.txt                        |  80 +++++++-------------------
 CMakeModules/FindLIBNUML.cmake        | 102 ++++++++++++++++++++++++++++++++++
 CMakeModules/FindLIBSBML.cmake        | 102 ++++++++++++++++++++++++++++++++++
 bindings/csharp/CMakeLists.txt        |  10 +++-
 bindings/java/CMakeLists.txt          |   5 +-
 bindings/java/Manifest.txt.in         |   2 +-
 bindings/perl/CMakeLists.txt          |   5 +-
 bindings/python/CMakeLists.txt        |  15 ++++-
 bindings/python/add_version.cmake     |  43 ++++++++++++++
 bindings/r/CMakeLists.txt             |   5 +-
 bindings/r/DESCRIPTION.in             |   4 +-
 bindings/ruby/CMakeLists.txt          |   5 +-
 sedml/CMakeLists.txt                  |  58 +++++++++++--------
 sedml/common/libsedml-package.h.cmake |   4 +-
 sedml/common/libsedml-version.h.cmake |   2 +-
 sedml/common/sedmlfwd.h               |   1 +
 16 files changed, 347 insertions(+), 96 deletions(-)
 create mode 100644 CMakeModules/FindLIBNUML.cmake
 create mode 100644 CMakeModules/FindLIBSBML.cmake
 create mode 100644 bindings/python/add_version.cmake
*commit*
ee18e6134d7b91adf9e96b079b011c805d3c32a5
--------------------------------------
build libSEDML
--------------------------------------
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for sbml-static
CMake Error at CMakeModules/FindLIBSBML.cmake:48 (message):
  libsbml include dir not found not found!
Call Stack (most recent call first):
  CMakeLists.txt:313 (find_package)


-- Configuring incomplete, errors occurred!
See also "/home/mkoenig/tmp/sedml_build/CMakeFiles/CMakeOutput.log".

Somehow the new CMakeModules/FindLIBSBML.cmake does not find libsbml.

The best
Matthias

pip package not installing on py3.6 on ubuntu

Hi all,
I just tried to install the python package on Ubuntu 16.04 via pip.
The installation is working, but when trying to import the package I get the following ImportError:

(sbmlutils) mkoenig@mkxps:~/git/sbmlutils$ pip install python-libsedml --force-reinstall --no-cache-dir
Collecting python-libsedml
  Downloading python-libsedml-0.4.1.tar.gz (2.9MB)
    100% |████████████████████████████████| 2.9MB 12.3MB/s 
Installing collected packages: python-libsedml
  Running setup.py install for python-libsedml ... done
Successfully installed python-libsedml-0.4.1
(sbmlutils) mkoenig@mkxps:~/git/sbmlutils$ python
Python 3.6.1+ (default, Jun  8 2017, 12:24:27) 
[GCC 5.4.1 20170519] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import libsedml
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/site-packages/libsedml/libsedml.py", line 28, in <module>
    _libsedml = swig_import_helper()
  File "/usr/local/lib/python2.7/site-packages/libsedml/libsedml.py", line 24, in swig_import_helper
    _mod = imp.load_module('_libsedml', fp, pathname, description)
  File "/home/mkoenig/envs/sbmlutils/lib/python3.6/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/home/mkoenig/envs/sbmlutils/lib/python3.6/imp.py", line 342, in load_dynamic
    return _load(spec)
ImportError: dynamic module does not define module export function (PyInit__libsedml)

Matthias

MATLAB bindings

I would like to request MATLAB bindings for this library! I would be happy to do any testing if necessary.

Update the default version?

Right now, the default level and version are 1 and 2 respectively (see here). Yet, the current version of SED-ML is L1V3 and L1V4 is around the corner. So, make sure to update the default version to 4 once L1V4 is out?

SedReader returns an error when parsing an algorithmParameter with an id attribute

Hi,

When trying to open a SED-ML file with the following simulation element:

<steadyState id="fba_1" name="fba_1">
  <algorithm kisaoID="KISAO:0000437">
    <listOfAlgorithmParameters>
      <algorithmParameter id="id1" kisaoID="KISAO:0000201" value="biomass_iRR1083"/>
      <algorithmParameter kisaoID="KISAO:0000201" value="maximize"/>
    </listOfAlgorithmParameters>
  </algorithm>
</steadyState>

... My instance of SedReader returns a 'Document does not conform to the Sed XML schema' error pointing to the first algorithmParameter element (it does not prevent me from using the resulting SedDocument object though). The error disappears when I remove the id attribute of the faulty element.

While investigating this behavior, I noticed that getters and setters for 'id' and 'name' attributes were disabled or commented out in SedBase class, making them inaccessible in several classes (including SedAlgorithm and SedAlgorithmParameter). Hence my questions:

Is the "disappearance" of those attributes related to my error?
Is there some refactoring going on around those attributes? Are they going to be illegal for several elements in future releases?

Best regards,
Bertrand

OS X: use RPATH to reference libSBML?

Right now, if you build libSEDML on OS X and then do otool -L libsedml.0.dylib, I get:

libsedml.0.dylib:
    libsedml.0.dylib (compatibility version 0.0.0, current version 0.3.1)
    libsbml.5.dylib (compatibility version 5.0.0, current version 5.13.0)
    /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

However, it would be much better (for deployment purposes), if we were to get:

libsedml.0.dylib:
    libsedml.0.dylib (compatibility version 0.0.0, current version 0.3.1)
    @rpath/libsbml.5.dylib (compatibility version 5.0.0, current version 5.13.0)
    /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

Sure, this can be done manually by calling install_name_tool -change libsbml.5.dylib @rpath/libsbml.5.dylib libsedml.0.dylib, but it would be nice if it could be done automatically.

create_sedml can't find numl

I told CMake about libnuml, and most things found it, but create_sedml didn't (on windows):

8>......\examples\c++\create_sedml.cpp(40): fatal error C1083: Cannot open include file: 'numl/NUMLTypes.h': No such file or directory

odd issue with setMath

Lucian reported the following issue:

I found an odd bug in libsedml that might have something to do with libsbml; I have no idea. Here's short code that demonstrates the problem:

SedDocument doc;
SedDataGenerator sdg = doc.createDataGenerator();
ASTNode astn = SBML_parseL3Formula("S1/S2");
sdg->setMath(astn);
ostringstream stream;
SedWriter sw;
sw.writeSedML(&doc, stream);
string v1 = stream.str();
stream.str("");
astn = SBML_parseL3Formula("log(S1/S2)");
sdg->setMath(astn->getChild(1));
sw.writeSedML(&doc, stream);
string v2 = stream.str();
assert(v1==v2);

Here's what I get for v1:

<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2"> <listOfDataGenerators> <dataGenerator> <apply> <divide/> <ci> S1 </ci> <ci> S2 </ci> </apply> </dataGenerator> </listOfDataGenerators> </sedML>

(which is correct)

and here's what I get for v2:

<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2"> <listOfDataGenerators> <dataGenerator> <apply> <divide/> <ci> S1 </ci> <ci> S2 </ci> </apply> </dataGenerator> </listOfDataGenerators> </sedML>

which is incorrect: it's missing the 'math' wrapper.
This is with SVN-libsbml compiled with all released packages, and not the legacy math.

Add version variable to python bindings

Is it possible to add the __version__ variable to the python libsedml bindings analogue to libsbml, i.e. support

import libsedml
print(libsedml.__version__)

Cannot build with namespace-enabled libSBML

I tried building libsedml against libsbml experimental (rev. 23207, last changed 23180) with namespaces enabled. I get the following error, which I believe is due to the fact that namespaces are enabled in this build of libsbml:

Building CXX object sedml/CMakeFiles/sedml.dir/SedChange.cpp.o
In file included from /home/poltergeist/devel/src/libsedml/sedml/SedChange.cpp:38:
In file included from /home/poltergeist/devel/src/libsedml/sedml/../sedml/SedTypes.h:75:
In file included from /home/poltergeist/devel/src/libsedml/sedml/../sedml/SedDocument.h:54:
In file included from /home/poltergeist/devel/src/libsedml/sedml/../sedml/SedDataDescription.h:54:
In file included from /home/poltergeist/devel/install/libnuml/include/numl/DimensionDescription.h:37:
In file included from /home/poltergeist/devel/install/libnuml/include/numl/AtomicDescription.h:32:
/home/poltergeist/devel/install/libnuml/include/numl/NMBase.h:218:11: error: reference to 'XMLNamespaces' is ambiguous
  virtual XMLNamespaces* getNamespaces() const ;
          ^
/home/poltergeist/devel/install/libnuml/include/numl/NMBase.h:58:7: note: candidate found by name lookup is 'XMLNamespaces'
class XMLNamespaces;
      ^
/home/poltergeist/devel/src/libsedml/sedml/../sedml/SedBase.h:166:7: note: candidate found by name lookup is 'libsbml::XMLNamespaces'
class XMLNamespaces;

There are many similar errors in the build output that I didn't show for brevity.

Add DWITH_CREATE_PYTHON_SOURCE=ON option to build python package

Opening this here to not forget about it.
See also https://mail.google.com/mail/u/0/#inbox/15acecacc2edbee8

logX and logY not required on plot in L1V2

Hi Frank,
with the latest version of libSEDML I get validation warnings on L1V2 documents of the form:

    cls.checkSEDMLDocument(doc)
  File "/home/mkoenig/git/tellurium/tellurium/sedml/tesedml.py", line 1553, in checkSEDMLDocument
    raise IOError(doc.getErrorLog().toString())
IOError: line 50: (01015 [Error]) Missing a required XML attribute. The plot2D attribute 'logX' is required.

line 50: (01015 [Error]) Missing a required XML attribute. The plot2D attribute 'logY' is required.

These attributes are not required in L1V2.
Example to reproduce which should be valid SED-ML L1V2.

<?xml version="1.0" encoding="UTF-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
  <listOfSimulations>
    <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="100">
      <algorithm kisaoID="KISAO:0000019"/>
    </uniformTimeCourse>
  </listOfSimulations>
  <listOfModels>
    <model id="model1" language="urn:sedml:language:sbml.level-3.version-1" source="myModel.xml"/>
  </listOfModels>
  <listOfTasks>
    <task id="task1" modelReference="model1" simulationReference="sim1"/>
  </listOfTasks>
  <listOfDataGenerators>
    <dataGenerator id="plot_0_0_0" name="time">
      <listOfVariables>
        <variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> time </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="plot_0_0_1" name="S1">
      <listOfVariables>
        <variable id="S1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=&apos;S1&apos;]" taskReference="task1" modelReference="model1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> S1 </ci>
      </math>
    </dataGenerator>
    <dataGenerator id="plot_0_1_1" name="S2">
      <listOfVariables>
        <variable id="S2" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=&apos;S2&apos;]" taskReference="task1" modelReference="model1"/>
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> S2 </ci>
      </math>
    </dataGenerator>
  </listOfDataGenerators>
  <listOfOutputs>
    <plot2D id="plot_0" name="Figure 1">
      <listOfCurves>
        <curve id="plot_0__plot_0_0_0__plot_0_0_1" logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_0_1"/>
        <curve id="plot_0__plot_0_0_0__plot_0_1_1" logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_1_1"/>
      </listOfCurves>
    </plot2D>
  </listOfOutputs>
</sedML>

The best
Matthias

Unable to read SED-ML file with csymbol definitionURL="http://sed-ml.org/#max"

Hi Frank,
I'm trying to read the SED-ML from your Combine archive example published with your paper here. It is the SED-ML included in the first supplementary file (also attached for reference). The problem seems to be caused by the http://sed-ml.org/#max csymbol definition. Here is the error output:

In SBML Level 2, the only values permitted for 'definitionURL' on a <csymbol> element are "http://www.sbml.org/sbml/symbols/time" and "http://www.sbml.org/sbml/symbols/delay". SBML Level 3 added "http://www.sbml.org/sbml/symbols/avogadro". SBML Level 3 Version 2 added "http://www.sbml.org/sbml/symbols/rateOf"
Reference: L3V2 Section 3.4.6
 The <csymbol> definitionURL 'http://sed-ml.org/#max' is not allowed for this level and version of SBML.

I am using libSEDML 0.4.2 built against libSBML 5.14.1 experimental from svn. I'm using the Python bindings.

repressilator-sedml.xml.txt

wrong URL to sed-ml.org in the header of some files

The version notes in the python bindings are pointing to http://sedml.org instead of http://sed-ml.org

C++ namespace issues building against libNuML w/out namespaces enabled

I think there are some problems when trying to build a namespace enabled libSEDML against libNuML (either with or without the namespaces enabled). Quick investigation looks like the problem might be the DimensionDescription forward declaration in sedmlfwd.h being wrapped with the LIBSEDML_CPP_NAMESPACE_BEGIN/END which puts it into the libsedml namespace.

Turning off namespaces in both libSEDML and libNuML gets things building.

Building libSEDML as a sub-project

When building the current version of libSEDML, it is assumed that the root folder of libSEDML will be used as the top level of the CMake source tree (i.e. the CMAKE_SOURCE_DIR variable in CMakeLists.txt files). However, it is not the case when building it as a sub-project (in this case, CMAKE_SOURCE_DIR would be higher in the project hierarchy); in such a configuration, the build would fail.

This problem can be solved by modifying several CMakeLists.txt files so that CMAKE_CURRENT_SOURCE_DIR is used instead of CMAKE_SOURCE_DIR when pointing to include directories.

conda support?

As I mentioned in an sbml-discussion poster a while back, we are currently moving our Python software deployment over to conda in the Sauro lab because it has better support for binary packages than pip. You've already ported libSBML to conda, which is very helpful, and I was wondering if it would be possible to do the same with libSEDML. conda support usually just involves adding a setup.py script plus a few extra files like meta.yaml (I presume this is how you implemented it in libSBML?). I would be happy to help with this if you like, just let me know.

Btw I'm aware of the pypi package for sedml, but it has the aforementioned problems with pip and it doesn't appear to be indexed in the Anaconda repository so I can't specify it as a dependency of other conda packages. Also, I tried installing it on the Mac and it took a very long time. Perhaps it is building from source. Regardless, we view installation time as part of the user experience and we want to minimize it. Tellurium has a lot of dependencies so fast installs are vital for us.

Special L1V4 version of libSEDML: reading a SED-ML file not working as expected!?

I am trying to read a valid (L1V2) SED-ML file using readSedML() and it all works fine using version 0.4.4 of libSEDML, but not using the special L1V4 version of libSEDML. After the call to readSedML(), I get what seems to be a valid SedDocument object, but then if I check some of its properties, I can see that mIsSetLevel, mIsSetVersion, mLevel and mVersion are set to false, false, 49 and 40, respectively while I would have expected true, true, 1 and 2, respectively (as is the case using version 0.4.4 of libSEDML). So, not sure what is going wrong here, but this might also explain issue #57?...

Issue with Python binding

I get following error when I try to build Python bindings for libSEDML.

Error 11 error LNK2019: unresolved external symbol "public: __thiscall NUMLConstructorException::NUMLConstructorException(void)" (??0NUMLConstructorException@@QAE@XZ) referenced in function __wrap_new_NUMLConstructorException C:\Lib\libSEDML-0.4.1\build\bindings\python\libsedml_wrap.obj binding_python_lib

It seems like it has something to do with linking. Any ideas?
I am working on Windows 7 using VS2013 with SWIG 3.0.10.

libsedmlcsP.dll

Hi all,

libsedmlcsP.dll registration error when i try to use gacutil:

gacutil -i build/bindings/csharp/libsedmlcsP.dll -f -package libsedml-sharp -root /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22.x86_64/usr/lib
Failure adding assembly build/bindings/csharp/libsedmlcsP.dll to the cache: Attempt to install an assembly without a strong name

Fedora 22 64bit,
libsedml 235bb5e,
full build log: https://gist.github.com/sagitter/5e941534afbf516431cf#file-libsedml-build_log

Thanks.

DataSource.indexSet functions behave strange

If no indexSet is set on a DataSource

ds.getIndexSet() returns `` instead of None (i.e. empty string)
ds.isSetIndexSet() returns true
This results in strange behavior if one does things like

if ds.getIndexSet() is None
or
if not ds.isSetIndexSet()

Kisao terms as ints?

It would be nice if there were kisao term set/get options that returned them by int, instead of by string. In fact, if the string versions went away entirely, I would not miss them.

Specifying logX and logY for plot2D

Hi Frank,

Relatively minor issue here. I was trying to read Combine archives exported by JWS Online. It appears to use the as yet unreleased version 3 of SED-ML. When I try to read their SED-ML, libSEDML complains that plot2D is missing logX and logY attributes (the child curves all have these set, but apparently plot2D requires it as well). If I simply add the missing logX and logY elements, then everything is fine.

The reason I'm posting this here is that the SED-ML Web Tools seem to work either way (with or without the logX/logY attributes). Do the web tools use the C# SED-ML library? If so, it looks like this might be a small discrepancy between the C#/C++ implementations.

Here is the original JWS archive (without the logX/logY attributes).

And here is the modified version where I manually inserted logX and logY:

[libsedml-0.4.3] csharp libraries: error CS0246

Hi all.

Following errors appear on s390x architectures when i compile csharp libraries of libsedml-0.4.3:

[ 85%] Build csharp files
cd /builddir/build/BUILD/libSEDML-0.4.3/build/bindings/csharp && /usr/bin/cmake -DCSHARP_EXTRA_ARGS="" -DCSHARP_COMPILER="/usr/bin/mcs" -DBIN_DIRECTORY="/builddir/build/BUILD/libSEDML-0.4.3/build/bindings/csharp" -DSRC_DIRECTORY="/builddir/build/BUILD/libSEDML-0.4.3/bindings/csharp" -P /builddir/build/BUILD/libSEDML-0.4.3/bindings/csharp/compile-native-files.cmake
Creating: libsedmlcsP.dll
csharp-files/XmlErrorStdVector.cs(14,48): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(158,54): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/ASTNodeList.cs(49,19): error CS0246: The type or namespace name `ASTNode' could not be found. Are you missing an assembly reference?
csharp-files/ASTNodeList.cs(53,10): error CS0246: The type or namespace name `ASTNode' could not be found. Are you missing an assembly reference?
csharp-files/ASTNodeList.cs(59,23): error CS0246: The type or namespace name `ASTNode' could not be found. Are you missing an assembly reference?
csharp-files/ASTNodeList.cs(63,10): error CS0246: The type or namespace name `ASTNode' could not be found. Are you missing an assembly reference?
csharp-files/CVTermList.cs(49,19): error CS0246: The type or namespace name `CVTerm' could not be found. Are you missing an assembly reference?
csharp-files/CVTermList.cs(53,10): error CS0246: The type or namespace name `CVTerm' could not be found. Are you missing an assembly reference?
csharp-files/CVTermList.cs(59,23): error CS0246: The type or namespace name `CVTerm' could not be found. Are you missing an assembly reference?
csharp-files/CVTermList.cs(63,10): error CS0246: The type or namespace name `CVTerm' could not be found. Are you missing an assembly reference?
csharp-files/DateList.cs(49,19): error CS0246: The type or namespace name `Date' could not be found. Are you missing an assembly reference?
csharp-files/DateList.cs(53,10): error CS0246: The type or namespace name `Date' could not be found. Are you missing an assembly reference?
csharp-files/DateList.cs(59,23): error CS0246: The type or namespace name `Date' could not be found. Are you missing an assembly reference?
csharp-files/DateList.cs(63,10): error CS0246: The type or namespace name `Date' could not be found. Are you missing an assembly reference?
csharp-files/ModelCreatorList.cs(49,19): error CS0246: The type or namespace name `SWIGTYPE_p_ModelCreator' could not be found. Are you missing an assembly reference?
csharp-files/ModelCreatorList.cs(53,10): error CS0246: The type or namespace name `SWIGTYPE_p_ModelCreator' could not be found. Are you missing an assembly reference?
csharp-files/ModelCreatorList.cs(59,23): error CS0246: The type or namespace name `SWIGTYPE_p_ModelCreator' could not be found. Are you missing an assembly reference?
csharp-files/ModelCreatorList.cs(63,10): error CS0246: The type or namespace name `SWIGTYPE_p_ModelCreator' could not be found. Are you missing an assembly reference?
csharp-files/OStream.cs(67,18): error CS0246: The type or namespace name `SWIGTYPE_p_std__ostream' could not be found. Are you missing an assembly reference?
csharp-files/SBaseList.cs(49,19): error CS0246: The type or namespace name `SBase' could not be found. Are you missing an assembly reference?
csharp-files/SBaseList.cs(53,10): error CS0246: The type or namespace name `SBase' could not be found. Are you missing an assembly reference?
csharp-files/SBaseList.cs(59,23): error CS0246: The type or namespace name `SBase' could not be found. Are you missing an assembly reference?
csharp-files/SBaseList.cs(63,10): error CS0246: The type or namespace name `SBase' could not be found. Are you missing an assembly reference?
csharp-files/SedBaseList.cs(49,19): error CS0246: The type or namespace name `SedBase' could not be found. Are you missing an assembly reference?
csharp-files/SedBaseList.cs(53,10): error CS0246: The type or namespace name `SedBase' could not be found. Are you missing an assembly reference?
csharp-files/SedBaseList.cs(59,23): error CS0246: The type or namespace name `SedBase' could not be found. Are you missing an assembly reference?
csharp-files/SedBaseList.cs(63,10): error CS0246: The type or namespace name `SedBase' could not be found. Are you missing an assembly reference?
csharp-files/SedNamespacesList.cs(49,19): error CS0246: The type or namespace name `SedNamespaces' could not be found. Are you missing an assembly reference?
csharp-files/SedNamespacesList.cs(53,10): error CS0246: The type or namespace name `SedNamespaces' could not be found. Are you missing an assembly reference?
csharp-files/SedNamespacesList.cs(59,23): error CS0246: The type or namespace name `SedNamespaces' could not be found. Are you missing an assembly reference?
csharp-files/SedNamespacesList.cs(63,10): error CS0246: The type or namespace name `SedNamespaces' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(140,107): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(16,11): error CS0246: The type or namespace name `HandleRef' could not be found. Are you missing `System.Runtime.InteropServices' using directive?
csharp-files/XmlErrorStdVector.cs(19,30): error CS0246: The type or namespace name `IntPtr' could not be found. Are you missing `System' using directive?
csharp-files/XmlErrorStdVector.cs(25,19): error CS0246: The type or namespace name `HandleRef' could not be found. Are you missing `System.Runtime.InteropServices' using directive?
csharp-files/XmlErrorStdVector.cs(30,19): error CS0246: The type or namespace name `HandleRef' could not be found. Are you missing `System.Runtime.InteropServices' using directive?
csharp-files/XmlErrorStdVector.cs(80,10): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(112,22): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(117,22): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(122,33): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(222,19): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(251,11): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(258,11): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(265,35): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(282,33): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(302,42): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(323,24): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(328,22): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(333,26): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(338,22): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
csharp-files/XmlErrorStdVector.cs(173,12): error CS0246: The type or namespace name `XMLError' could not be found. Are you missing an assembly reference?
Compilation failed: 51 error(s), 0 warnings
Creating: TestRunner.exe

Mono-4.8.0
Fedora 28 (development branch)
Full log: https://kojipkgs.fedoraproject.org//work/tasks/8132/22368132/build.log

libsedml python bindings overwrite libsbml python functionality

Importing libsedml in python overwrites the SBMLDocument.getModel functionality in libsbml, so that the libsbml model cannot be accessed any more.
See the attached example code (Ubuntu, x64, libsbml and libsedml build from latest commits with cmake).

from __future__ import print_function

sbml_str = """<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.8.1 on 2016-02-11 15:30 with libSBML version 5.12.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model id="test" name="test">
    <listOfCompartments>
      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="S1" compartment="default_compartment" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="S2" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k1" value="1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction id="J0" reversible="true" fast="false">
        <listOfReactants>
          <speciesReference species="S1" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S2" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k1 </ci>
              <ci> S1 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
"""

# load doc with libsbml
import libsbml
doc = libsbml.readSBMLFromString(sbml_str)
model = doc.getModel()
print(type(doc))
print(type(model))

print('*' * 80)  # Everything good until here

# importing libsedml overwrites the libsbml.getModel !!!
# suddenly libsedml.Model is returned when calling getModel on doc !
import libsedml

model = doc.getModel()
print(type(doc))
print(type(model))  # <class 'libsedml.Model'> ??

# not even this works any more
model = libsbml.SBMLDocument.getModel(doc)
print(type(model))  # <class 'libsedml.Model'>

print(libsbml.__version__)  # Updated to revision 22780
print(libsedml.getLibSEDMLVersion())  # commit 31d92030c91e21d9db7

Results in

<class 'libsbml.SBMLDocument'>
<class 'libsedml.Model'>
********************************************************************************
<class 'libsbml.SBMLDocument'>
<class 'libsedml.Model'>
<class 'libsedml.Model'>
5.12.1
401

I.e. after importing libsedml I cannot access the libsbml model from an SBMLDocument any more.

Numl functions not working with python bindings

Hi Frank,
trying to read the numl data with the libsedml python bindings does not work. Somehow the numl related functions are not callable via the python interface, despite them being visible (i.e. I can see the documention and the function via the IDE)
(installed via pip install python-libsedml, version 0.4.1, or via the wheel Kyle build from develop version)

When trying to call functions on the NumlDocument I get:

/home/mkoenig/envs/tellurium-py27/bin/python /home/mkoenig/git/tellurium/tellurium/oven/sedmldata/reading_numl.py
Traceback (most recent call last):
  File "/home/mkoenig/git/tellurium/tellurium/oven/sedmldata/reading_numl.py", line 85, in <module>
    df_numl = load_numl_data(SOURCE_NUML)
  File "/home/mkoenig/git/tellurium/tellurium/oven/sedmldata/reading_numl.py", line 63, in load_numl_data
    print(doc_numl.getNumResultComponents())
AttributeError: 'SwigPyObject' object has no attribute 'getNumResultComponents'
Version: 0.4.1
<Swig Object of type 'NUMLDocument_t *' at 0x7f41d6f06de0>

Example attached.
sedmldata.tar.gz

The best
Matthias

[Python wrappers] SedVectorRange values

Hi,
Working on RepeatedTask execution, it appears that getValues() method from SedVectorRange class returns a Swig object of type std::vector, which cannot be directly used in Python:

>>> reader = libsedml.SedReader()
>>> doc = reader.readSedML('test_repeated_task_vector.xml')
>>> r_task = doc.getTask(1)
>>> r_task
<libsedml.SedRepeatedTask; proxy of <Swig Object of type 'SedRepeatedTask_t *' at 0x9030518> >
>>> v_range = r_task.getRange('current')
>>> v_range
<libsedml.SedVectorRange; proxy of <Swig Object of type 'SedVectorRange_t *' at 0x90304e8> >
>>> v_range.getNumValues()
5
>>> v_range.getValues()
<Swig Object of type 'std::vector< double > *' at 0x90305a8>

The test_repeated_task_vector.xml file I use contains the following listOfTasks element:

<listOfTasks>
  <task id="task_1" name="task_1" modelReference="febs_model" simulationReference="simulation_1">
  </task>
  <repeatedTask id="task_2" resetModel="true" range="current">
    <listOfRanges>
      <vectorRange id="current">
        <value>5.0</value>
        <value>5.5</value>
        <value>6.0</value>
        <value>6.5</value>
        <value>7.0</value>
      </vectorRange>
    </listOfRanges>
    <listOfChanges>
      <setValue target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k1']/@value" range="current" modelReference="febs_model">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci>current</ci>
        </math>
      </setValue>
    </listOfChanges>
    <listOfSubTasks>
      <subTask order="1" task="task_1" />
    </listOfSubTasks>
  </repeatedTask>
</listOfTasks>

Is there a way to workaround this problem?
Best regards,
Bertrand

Python bindings: ImportError: dynamic module does not define init function (init_libsedml)

The python bindings do not work on ubuntu linux any more.
There is some ImportError, probably due to some naming issues between _libsedml and libsedml in the swig bindings.

 import libsedml
  File "/usr/local/lib/python2.7/site-packages/libsedml/libsedml.py", line 28, in <module>
    _libsedml = swig_import_helper()
  File "/usr/local/lib/python2.7/site-packages/libsedml/libsedml.py", line 24, in swig_import_helper
    _mod = imp.load_module('_libsedml', fp, pathname, description)
ImportError: dynamic module does not define init function (init_libsedml)

I had the same issues with antimony at some point (everything worked fine on win, but on linux the distinction between _antimony and antimony matter in the Swig bindings.

Add non-const version of 'getAlgorithm'

There is only a const version of SedSimulation::getAlgorithm. There should be a non-const version as well.

R package only building when deleting build folder

Hi all,
The R package for libSEDML only builds when I delete the old build folder. When I just try to rebuild without deleting I get the error messages below.

-- Build files have been written to: /home/mkoenig/tmp/sedml_build
...
[ 96%] Built target binding_python_lib
[ 97%] Create R Package (64bit)
[ 99%] Built target example_cpp_create_sedml
DONE
* installing *source* package ‘libSEDML’ ...
mv: cannot move '/home/mkoenig/tmp/sedml_build/bindings/r/temp/libSEDML' to '/home/mkoenig/tmp/sedml_build/bindings/r/temp/00LOCK-libSEDML/libSEDML': Permission denied
Warning in file.copy(f, instdir, TRUE) :
  problem copying ./NAMESPACE to /home/mkoenig/tmp/sedml_build/bindings/r/temp/libSEDML/NAMESPACE: Permission denied
Warning in file(file, if (append) "a" else "w") :
  cannot open file '/home/mkoenig/tmp/sedml_build/bindings/r/temp/libSEDML/DESCRIPTION': Permission denied
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘libSEDML’
bindings/r/CMakeFiles/binding_r_package.dir/build.make:69: recipe for target 'bindings/r/libSEDML_042.zip' failed
make[2]: *** [bindings/r/libSEDML_042.zip] Error 1
CMakeFiles/Makefile2:468: recipe for target 'bindings/r/CMakeFiles/binding_r_package.dir/all' failed
make[1]: *** [bindings/r/CMakeFiles/binding_r_package.dir/all] Error 2
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2

I use

cmake -DEXTRA_LIBS="xml2;z;bz2;" -DWITH_EXAMPLES=ON -DWITH_JAVA=ON -DWITH_PYTHON=ON -DWITH_R=ON ${GIT_DIR}/$SEDMLCODE
# cmake -DEXTRA_LIBS="xml2;z;bz2;" -DWITH_EXAMPLES=ON -DWITH_JAVA=ON -DWITH_PYTHON=ON -DWITH_R=ON -DPYTHON_EXECUTABLE="/usr/bin/python" -DPYTHON_INCLUDE_DIR="/usr/include/python2.7" -DPYTHON_LIBRARY="/usr/lib/x86_64-linux-gnu/libpython2.7.so" ${GIT_DIR}/$SEDMLCODE
rc=$?; if [[ $rc != 0 ]]; then exit $rc; fi

make -j8
sudo make install

R bindings
priority: low
Ubuntu 16.04
Workaround: delete the build folder before building

Matthias

CMake output seems to have some left over libSBML text

When configuring the build with CMake you get a nice summary of the configuration, but some of the links seem to be set up more for libsbml than libSEDML.

e.g.,

More information and the latest version are available online at
http://sbml.org/Software/libSEDML

Please report problems using the issue tracker at
http://sbml.org/Software/libsedml/issue-tracker

Reading attached SED-ML file kills python kernel

Hi Frank,
Reading the attached SED-ML file kills the python kernel (zipped so I can upload on github)
test-sedml.xml.zip

import libsedml

if __name__ == "__main__":
    path = "test-sedml.xml"
    doc = libsedml.readSedMLFromFile(path)

Results in

Process finished with exit code 139 (interrupted by signal 11: SIGSEGV)

This is part of a larger problem and comes up from time to time:
If somehow possible the C++ libraries should never sys.exit(), no matter what goes wrong.
The sys.exit() is extremely difficult to handle from the python side, because I cannot catch this in a Exception or anything. When I am running for instance libsedml code on a python server, this example kills the complete web application. The only way to recover is to monitor the server and restart the python processes if libsedml, libsbml ... forced an exit.

The best
Matthias

Missing includes in bindings/swig/libsedml.i?

Having updated my libSEDML version today (hence the spam - sorry for that), I noticed that several new classes (such as SedAddXML or SedChangeXML) were not included in the bindings/swig/libsedml.i file, and are therefore not available when wrapping the library.

libSEDML Java bindings not building with latest libnuml

Hi Frank,

I tried to update libsedml to the latest commit. With the latest changes in libnuml the JAVA swig bindings are not building any more.

I get the following errors

[ 81%] Built target sedml-static
Scanning dependencies of target binding_java_swig
[ 82%] Swig Java source
/usr/local/include/numl/NUMLNamespaces.h:162: Error: Syntax error in input(3).
make[2]: *** [bindings/java/libsedml_wrap.cpp] Error 1
make[1]: *** [bindings/java/CMakeFiles/binding_java_swig.dir/all] Error 2
make: *** [all] Error 2

The full log and build script I am using are attached.
I am on Ubuntu 14.04 LTS 64bit.

libsedml_logs.zip

Matthias

VERSION.txt is 0.4.2 but getLibSEDMLDottedVersion returns "1.0.1"

I'm getting "1.0.1" from getLibSEDMLDottedVersion, which is different than what I expected. I don't know why. Any help would be appreciated. The VERSION.txt file in the the source dir says 0.4.2 (which matches the GitHub repo). Here is my generated common/libsedml-version.h file. I am on CentOS 5 w/ gcc 4.8.

/**
 * @file    libsedml-version.h
 * @brief   Define libSEDML version numbers for access from client software.
 *
 * <!--------------------------------------------------------------------------
 *
 * This file is part of libSEDML.  Please visit http://sed-ml.org for more
 * information about SED-ML. The latest version of libSEDML can be found on 
 * github: https://github.com/fbergmann/libSEDML/
 * 
 * 
 * Copyright (c) 2013-2014, Frank T. Bergmann  
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met: 
 * 
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer. 
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution. 
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 * 
 * ---------------------------------------------------------------------- -->
 */

#ifndef LIBSEDML_VERSION_H
#define LIBSEDML_VERSION_H 

#include <sedml/common/extern.h>


/**
 * LIBSEDML_DOTTED_VERSION:
 *
 * A version string of the form "1.2.3".
 */
#define LIBSEDML_DOTTED_VERSION	"1.0.1"


/**
 * LIBSEDML_VERSION:
 *
 * The version as an integer: version 1.2.3 becomes 10203.  Since the major
 * number comes first, the overall number will always increase when a new
 * libSEDML is released, making it easy to use less-than and greater-than
 * comparisons when testing versions numbers.
 */
#define LIBSEDML_VERSION		402


/**
 * LIBSEDML_VERSION_STRING:
 *
 * The numeric version as a string: version 1.2.3 becomes "10203".
 */
#define LIBSEDML_VERSION_STRING	"402"


LIBSEDML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS

/**
 * Returns the version number of this copy of libSEDML as an integer.
 *
 * @return the libSEDML version as an integer; version 1.2.3 becomes 10203.
 */
LIBSEDML_EXTERN
int 
getLibSEDMLVersion ();


/**
 * Returns the version number of this copy of libSEDML as a string.
 *
 * @return the libSEDML version as a string; version 1.2.3 becomes
 * "1.2.3".
 *
 * @see getLibSEDMLVersionString()
 */
LIBSEDML_EXTERN
const char* 
getLibSEDMLDottedVersion ();


/**
 * Returns the version number of this copy of libSEDML as a string without
 * periods.
 *
 * @return the libSEDML version as a string: version 1.2.3 becomes "10203".
 *
 * @see getLibSEDMLDottedVersion()
 */
LIBSEDML_EXTERN
const char* 
getLibSEDMLVersionString ();


END_C_DECLS
LIBSEDML_CPP_NAMESPACE_END

#endif  /* LIBSEDML_VERSION_H */

Ruby bindings always failed on Fedora

Hi all.

Ruby bindings of libsedml-0.4.4 are always failing on Fedora with this message:

BUILDSTDERR: /builddir/build/BUILD/libSEDML-0.4.4/build/bindings/ruby/libsedml_wrap.cpp: In function 'VALUE _wrap_XMLErrorLog_add(int, VALUE*, VALUE)':
BUILDSTDERR: /builddir/build/BUILD/libSEDML-0.4.4/build/bindings/ruby/libsedml_wrap.cpp:5075:28: warning: 'argv[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:        if (rb_obj_is_kind_of(obj, rb_cArray) == Qtrue) {
BUILDSTDERR:            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/libSEDML-0.4.4/build/bindings/ruby/libsedml_wrap.cpp:28658:9: note: 'argv[1]' was declared here
BUILDSTDERR:    VALUE argv[3];
BUILDSTDERR:          ^~~~
BUILDSTDERR: /builddir/build/BUILD/libSEDML-0.4.4/build/bindings/ruby/libsedml_wrap.cpp: In function 'VALUE _wrap_SedErrorLog_add(int, VALUE*, VALUE)':
BUILDSTDERR: /builddir/build/BUILD/libSEDML-0.4.4/build/bindings/ruby/libsedml_wrap.cpp:1374:83: warning: 'argv[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:  #define SWIG_ConvertPtr(obj, pptr, type, flags)         SWIG_Ruby_ConvertPtrAndOwn(obj, pptr, type, flags, 0)
BUILDSTDERR:                                                                                    ^
BUILDSTDERR: /builddir/build/BUILD/libSEDML-0.4.4/build/bindings/ruby/libsedml_wrap.cpp:31489:9: note: 'argv[1]' was declared here
BUILDSTDERR:    VALUE argv[3];
BUILDSTDERR:          ^~~~
BUILDSTDERR: cc1plus: some warnings being treated as errors

Dependencies list; https://kojipkgs.fedoraproject.org//work/tasks/9137/33689137/root.log
Build log is attached.

error when compiling java bindings

Disclaimer: I modified the CMakeLists.txt to use find_library/find_path, which were commented out, instead of find_package as I could not find the appropriate cmake files in my libSBML installiation an thus not pass an appropriate CMAKE_PREFIX_PATH. But, I hope this does not lead to the error that I encounter.

To build sedml I used the following command for cmake

cmake .. -DEXTRA_LIBS='xml2;bz2;z;iconv'  -DLIBSBML_LIBRARY='/usr/local/lib/libsbml.dylib' -DLIBSBML_INCLUDE_DIR='/usr/local/include/' -DLIBNUML_LIBRARY='/usr/local/lib/libnuml.dylib' -DLIBNUML_INCLUDE_DIR='/usr/local/include/' -DWITH_JAVA=ON

When I subsequently call make, the sedml and sedml-static targets build fine, but for the binding_java_swig I encounter the following error:

Scanning dependencies of target binding_java_swig
[ 95%] Swig Java source
/Users/F.Froehlich/Documents/MATLAB/libSEDML/bindings/java/../../sedml/common/sedmlfwd.h:353: Error: Syntax error in input(1).
make[2]: *** [bindings/java/libsedml_wrap.cpp] Error 1
make[1]: *** [bindings/java/CMakeFiles/binding_java_swig.dir/all] Error 2

When I compile everything without java bindings compilation works fine.

Special L1V4 version of libSEDML: crashes when trying to retrieve the number of errors in an error log

I have some very simple test code:

libsedml::SedErrorLog *errorLog = sedmlDocument->getErrorLog();
qDebug("sedmlDocument->getNumErrors(): %d", sedmlDocument->getNumErrors());
qDebug("errorLog->getNumErrors():      %d", errorLog->getNumErrors());

The first line goes through fine (but errorLog's address looks dodgy to me), and so does the second line (it tells me that my SED-ML document has no errors, which is indeed correct). However, the third line crashes OpenCOR.

FWIW, the same code works perfectly fine using version 0.4.4 of libSEDML.

Create no timestamp when creating SEDML

No timestamp should be inserted when writing SEDML

I create a large amount of files on the fly with antimony and phrasedml which are managed in repositories. Due to the timestamps every commit has 100s of files, because all the changes in the timestamps are part of the commits. Even if nothing changed in the files.

I also wrote timestamps & model histories in my files before, but it creates more problems than it is useful. Having the files in a repository is a much better solution and one can always access the exact time of creation/modification.
If one wants timestamps in the files one can write a model history/annotation which contains the information, but it should not be inserted by default.

Special L1V4 version of libSEDML: update the default version to L1V4

Right now, if you create a new SED-ML document using the special L1V4 version of libSEDML, it will have a level/version of L1V3 while one would expect it to have a level/version of L1V4.

Swig language interfaces cannot be build due to missing *.h

When trying to build libsedml with

cmake -DEXTRA_LIBS="xml2;z;bz2;" -DWITH_EXAMPLES=ON -DWITH_JAVA=ON -DWITH_PYTHON=ON -DWITH_R=ON -DLIBSBML_INCLUDE_DIR="/usr/local/include/sbml" -DLIBNUML_INCLUDE_DIR="/usr/local/include/numl" ${GIT_DIR}/$SEDMLCODE

the build of the language bindings (Java, python & R) fails due to missing sbml and numl *.h files.
See build logs and error messages below.

This is probably related to #39

In addition when showing the library overview of the build the numl library shows the sbml library, i.e.

NUML library configuration:
     NUML library                  = /usr/local/lib/libsbml-static.a

Build log

--------------------------------------
build libSEDML
--------------------------------------
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for sbml-static
-- Found LIBSBML: sbml-static  
-- Looking for numl-static
-- Found LIBNUML: numl-static  
-- Looking for gzopen in /usr/lib/x86_64-linux-gnu/libz.so
-- Looking for gzopen in /usr/lib/x86_64-linux-gnu/libz.so - found
-- Looking for include file check.h
-- Looking for include file check.h - not found
-- Looking for include file expat.h
-- Looking for include file expat.h - found
-- Looking for include file errno.h
-- Looking for include file errno.h - found
-- Looking for include file ieeefp.h
-- Looking for include file ieeefp.h - not found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file float.h
-- Looking for include file float.h - found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found SWIG: /usr/bin/swig (found version "3.0.8") 
-- Found JNI: /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjawt.so  
-- Found Java: /usr/lib/jvm/java-8-oracle/bin/java (found version "1.8.0.101") found components:  Development 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.5m.so (found version "3.5.2") 
-- Found PythonInterp: /usr/bin/python3.5 (found version "3.5.2") 
CMake Warning (dev) at bindings/r/CMakeLists.txt:262 (get_target_property):
  Policy CMP0026 is not set: Disallow use of the LOCATION target property.
  Run "cmake --help-policy CMP0026" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The LOCATION property should not be read from target "binding_r_lib".  Use
  the target name directly with add_custom_command, or use the generator
  expression $<TARGET_FILE>, as appropriate.

This warning is for project developers.  Use -Wno-dev to suppress it.

-- 
----------------------------------------------------------------------
libSEDML version 0.4.2
----------------------------------------------------------------------

   More information and the latest version are available online at
   https://github.com/fbergmann/libSEDML/

   Please report problems using the issue tracker at
   https://github.com/fbergmann/libSEDML/issues

   To contact the developers directly, email [email protected]

   Configured on host 'core1'
     host type                     = Linux
     host operating system         = Linux 4.4.0-59-generic
     host CPU architecture         = x86_64

   General build flags:
     CC                            = /usr/bin/cc
     CXX                           = /usr/bin/c++
     CPPFLAGS                      =  -DLINUX -DPACKAGE_VERSION="0.4.2"  -DPACKAGE_NAME="libsedml"
     CFLAGS                        =  -fno-strict-aliasing -fPIC
     CXXFLAGS                      =  -fno-strict-aliasing -fPIC
     LDFLAGS                       = 

   SBML library configuration:
     SBML library                  = /usr/local/lib/libsbml-static.a
     SBML include                  = -I/usr/local/include/sbml

   NUML library configuration:
     NUML library                  = /usr/local/lib/libsbml-static.a
     NUML include                  = -I/usr/local/include/numl

  Other libSEDML configuration settings:
     Installation $prefix          = /usr/local
--   Value of $LD_LIBRARY_PATH     = :/usr/local/lib/cellml-sdk-1.13-Linux-x86_64/lib:/home/mkoenig/Programs/gurobi652/linux64/lib
--   Using SWIG                    = /usr/bin/swig
--   Using Java                    = /usr/lib/jvm/java-8-oracle/bin/java
--   Using Python                  = /usr/bin/python3.5
-- 

--   Using C++ namespace for libSEDML (libsedml) = no
-- 
----------------------------------------------------------------------
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mkoenig/tmp/sedml_build
Scanning dependencies of target binding_python_swig
Scanning dependencies of target binding_r_swig
Scanning dependencies of target binding_java_swig
[  1%] Swig Python source
[  1%] Swig R source
[  1%] Swig Java source
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:66: Error: Unable to find 'sbml/common/extern.h'
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:67: Error: Unable to find 'sbml/xml/XMLExtern.h'
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:387: Error: Unable to find 'sbml/common/libsbml-version.h'
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:388: Error: Unable to find 'sbml/common/operationReturnValues.h'
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:393: Error: Unable to find 'sbml/xml/XMLError.h'
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:395: Error: Unable to find 'sbml/xml/XMLErrorLog.h'
/home/mkoenig/git/libSEDML/bindings/r/../swig/libsedml.i:66: Error: Unable to find 'sbml/common/extern.h'
/home/mkoenig/git/libSEDML/bindings/r/../swig/libsedml.i:67: Error: Unable to find 'sbml/xml/XMLExtern.h'
/home/mkoenig/git/libSEDML/bindings/python/../swig/libsedml.i:66: Error: Unable to find 'sbml/common/extern.h'
/home/mkoenig/git/libSEDML/bindings/python/../swig/libsedml.i:67: Error: Unable to find 'sbml/xml/XMLExtern.h'
/home/mkoenig/git/libSEDML/bindings/java/../swig/libsedml.i:443: Error: Unable to find 'sbml/math/MathML.h'
...

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