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#1 Building on Ubuntu 12.04 or later

1.0
open
nobody
None
2015-01-27
2014-07-08
Erik
No

Hello!

I've been asked by a journal reviewer to compare my forward modelling toolbox (http://cyclotronresearchcentre.github.io/forward/) against SimBio / NeuroFEM. The problem I'm having is that I am utterly unable to build the software. I have tried on both Mac OSX 10.9.3 and Ubuntu 12.04.4 LTS using the instructions from here: 

https://www.mrt.uni-jena.de/simbio/index.php/Compiling_SimBio

I tried using the Ubuntu 10.04 instructions, followed by the updates for 11.04, to no avail. It seems that the switch in trunk/toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp for
"integer comsol" to "uint32" is giving me an error, though I am clueless as to why. I get that "‘uint32’ was not declared in this scope" when using "make" on neurofem.

mpiCC  -g -DMPICH_IGNORE_CXX_SEEK -DTESTSUITE  -c  -o  SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.o ../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp -I../neurofem/include/ -I../neurofem/include/colsamm/ -I../toolbox/linearalgebra/pebbles/libsrc/ -I../toolbox/linearalgebra/pebbles/libsrc/integrator/ -I../toolbox/linearalgebra/pebbles/libsrc/matrix/ -I../toolbox/linearalgebra/pebbles/libsrc/parallel/ -I../toolbox/linearalgebra/pebbles/libsrc/prepro/  -I../toolbox/linearalgebra/pebbles/libsrc/setup/ -I../toolbox/linearalgebra/pebbles/libsrc/solver/ -I../toolbox/linearalgebra/pebbles/pebbles/ -I../ipm_toolbox/inverse/ -I../ipm_toolbox/statistics/ -I../ipm_toolbox/signalproc/ -I../ipm_toolbox/breakcriteria/ -I../toolbox/signalproc/ -I../ipm_toolbox/errorest/ -I../ipm_toolbox/goalfunctions/ -I../ipm_toolbox/grid/ -I../ipm_toolbox/initialguess/ -I../toolbox/weighter/ -I../ipm_toolbox/optimizer/ -I../ipm_toolbox/regularizer/ -I../ipm_toolbox/searchvolume/ -I../ipm_toolbox/simulator/ -I../ipm_toolbox/weighter/ -I../toolbox/ -I../toolbox/inverse/ -I../ipm_toolbox/simulator/bem/ -I../toolbox/grid/ -I../ipm_toolbox/optimizer/marquardt/ -I../ipm_toolbox/optimizer/simplex/ -I../ipm_toolbox/simulator/analytic/ -I../misc/ -I../converters/RES4toNeuroFEM/ -I../converters/RES4toNeuroFEM/ByteSwap/ -I../converters/RES4toNeuroFEM/ReadRES4/ -I../converters/RES4toNeuroFEM/Sensor/ -I../converters/RES4toNeuroFEM/Sensortype/ -I../converters/RES4toNeuroFEM/System/ -I../converters/RES4toNeuroFEM/System/include/ -I../toolbox/goalfunctions/ -I../inverse/ -I../toolbox/inverse/beamf/ -I../toolbox/statistics/ -I../toolbox/simulator/fem/ -I../toolbox/utilities/ -I../toolbox/fileio/ -I../toolbox/datatypes/ -I../toolbox/container/ -I../neurofem/converters/gmv_to_geoknw/ -I../neurofem/converters/img2mesh/ -I../misc/neurofem/colsamm/ -I../misc/neurofem/ -I../application/uif/ -I../toolbox/linearalgebra/ -I../toolbox/fileio/vista/ -ansi -I../toolbox/linearalgebra/pebbles/libsrc
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp: In member function ‘void SIM_SimulatorEEGMEGNeuroFEMParPiluts_c::prepareSimulator()’:
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp:110:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp: In member function ‘virtual void SIM_SimulatorEEGMEGNeuroFEMParPiluts_c::forwardSimulation(doublereal*, integer, integer*, integer*, doublereal*)’:
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp:203:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp: In member function ‘void SIM_SimulatorEEGMEGNeuroFEMParPiluts_c::forwardSimulationChild()’:
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp:399:40: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp: In member function ‘void SIM_SimulatorEEGMEGNeuroFEMParPiluts_c::callParPiluts()’:
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp:1274:20: error: ‘uint32’ was not declared in this scope
make: *** [SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.o] Error 1

Trying to make Subtraction, PartialIntegration, or Venant in the SimBio trunk also fails. Some of the errors appear to be related to the recommended changes (e.g. in save ma,inext,inextp). Can someone clarify if this line is MEANT to be commented out in the "new code" block? Why not just remove it?

➜  trunk  make Subtraction
cp neurofem/Makefile_linux_dbx_subtraction neurofem/Makefile
making all in /Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles...
make[1]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles'
mkdir -p lib/lib_linux_dbx
cd pebbles; make
make[2]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/pebbles'
make[3]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/matrix'
make[3]: Nothing to be done for `libgoal'.
make[3]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/matrix'
make[3]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/setup'
make[3]: Nothing to be done for `libgoal'.
make[3]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/setup'
make[3]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/prepro'
make[3]: Nothing to be done for `libgoal'.
make[3]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/prepro'
make[3]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/solver'
make[3]: Nothing to be done for `libgoal'.
make[3]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/solver'
make[3]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/parallel'
make[3]: Nothing to be done for `libgoal'.
make[3]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/libsrc/parallel'
done
mpiCC  -o pebbles pebbles.o src/simulate.o  -L../lib/lib_linux_dbx   -lprepro -lsolver  -lmatrix  -lsetup -lparallel  -lm -lstdc++
make[2]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles/pebbles'
make[1]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/pebbles'
making all in /Code/neurofem-simbio-code/trunk/neurofem...
make[1]: Entering directory `/Code/neurofem-simbio-code/trunk/neurofem'
mpiCC  -g -w  -DTESTSUITE -DMPICH_IGNORE_CXX_SEEK    -c  -o  SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.o ../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp -I../neurofem/include/ -I../neurofem/include/colsamm/ -I../toolbox/linearalgebra/pebbles/libsrc/ -I../toolbox/linearalgebra/pebbles/libsrc/integrator/ -I../toolbox/linearalgebra/pebbles/libsrc/matrix/ -I../toolbox/linearalgebra/pebbles/libsrc/parallel/ -I../toolbox/linearalgebra/pebbles/libsrc/prepro/  -I../toolbox/linearalgebra/pebbles/libsrc/setup/ -I../toolbox/linearalgebra/pebbles/libsrc/solver/ -I../toolbox/linearalgebra/pebbles/pebbles/ -I../ipm_toolbox/inverse/ -I../ipm_toolbox/statistics/ -I../ipm_toolbox/signalproc/ -I../ipm_toolbox/breakcriteria/ -I../toolbox/signalproc/ -I../ipm_toolbox/errorest/ -I../ipm_toolbox/goalfunctions/ -I../ipm_toolbox/grid/ -I../ipm_toolbox/initialguess/ -I../toolbox/weighter/ -I../ipm_toolbox/optimizer/ -I../ipm_toolbox/regularizer/ -I../ipm_toolbox/searchvolume/ -I../ipm_toolbox/simulator/ -I../ipm_toolbox/weighter/ -I../toolbox/ -I../toolbox/inverse/ -I../ipm_toolbox/simulator/bem/ -I../toolbox/grid/ -I../ipm_toolbox/optimizer/marquardt/ -I../ipm_toolbox/optimizer/simplex/ -I../ipm_toolbox/simulator/analytic/ -I../misc/ -I../converters/RES4toNeuroFEM/ -I../converters/RES4toNeuroFEM/ByteSwap/ -I../converters/RES4toNeuroFEM/ReadRES4/ -I../converters/RES4toNeuroFEM/Sensor/ -I../converters/RES4toNeuroFEM/Sensortype/ -I../converters/RES4toNeuroFEM/System/ -I../converters/RES4toNeuroFEM/System/include/ -I../toolbox/goalfunctions/ -I../inverse/ -I../toolbox/inverse/beamf/ -I../toolbox/statistics/ -I../toolbox/simulator/fem/ -I../toolbox/utilities/ -I../toolbox/fileio/ -I../toolbox/datatypes/ -I../toolbox/container/ -I../neurofem/converters/gmv_to_geoknw/ -I../neurofem/converters/img2mesh/ -I../misc/neurofem/colsamm/ -I../misc/neurofem/ -I../application/uif/ -I../toolbox/linearalgebra/ -I../toolbox/fileio/vista/ -ansi -I../toolbox/linearalgebra/pebbles/libsrc
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp: In member function ‘void SIM_SimulatorEEGMEGNeuroFEMParPiluts_c::callParPiluts()’:
../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.cpp:1274:20: error: ‘uint32’ was not declared in this scope
make[1]: *** [SIM_SimulatorEEGMEGNeuroFEMParPiluts_c.o] Error 1
make[1]: Leaving directory `/Code/neurofem-simbio-code/trunk/neurofem'
making all in /Code/neurofem-simbio-code/trunk/neurofem/lib...
make[1]: Entering directory `/Code/neurofem-simbio-code/trunk/neurofem/lib'
make -C ../../toolbox/linearalgebra/blas LIBDIR=/Code/neurofem-simbio-code/trunk/neurofem/lib FFLAGS=-g CFLAGS=-g AR=ar FC=g77 CC=gcc MAKE=make RANLIB=ranlib SUFFIX=_linux_dbx
make[2]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/blas'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/blas'
make -C ../../toolbox/simulator/fem/fofu LIBDIR=/Code/neurofem-simbio-code/trunk/neurofem/lib FFLAGS=-g CFLAGS=-g AR=ar FC=g77 CC=gcc MAKE=make RANLIB=ranlib SUFFIX=_linux_dbx
make[2]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/simulator/fem/fofu'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/simulator/fem/fofu'
make -C ../../misc/ime LIBDIR=/Code/neurofem-simbio-code/trunk/neurofem/lib FFLAGS=-g CFLAGS=-g AR=ar FC=g77 CC=gcc MAKE=make RANLIB=ranlib SUFFIX=_linux_dbx SYS=linux
make[2]: Entering directory `/Code/neurofem-simbio-code/trunk/misc/ime'
make[2]: `/Code/neurofem-simbio-code/trunk/neurofem/lib/libime_linux_dbx.a' is up to date.
make[2]: Leaving directory `/Code/neurofem-simbio-code/trunk/misc/ime'
make -C ../../toolbox/linearalgebra/lapack LIBDIR=/Code/neurofem-simbio-code/trunk/neurofem/lib FFLAGS=-g CFLAGS=-g AR=ar FC=g77 CC=gcc RANLIB=ranlib SUFFIX=_linux_dbx
make[2]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/lapack'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/lapack'
make -C ../../toolbox/linearalgebra/libsol LIBDIR=/Code/neurofem-simbio-code/trunk/neurofem/lib FFLAGS=-g CFLAGS=-g AR=ar FC=g77 CC=gcc MAKE=make RANLIB=ranlib SUFFIX=_linux_dbx
make[2]: Entering directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/libsol'
g77 -c -g ransol.f
ransol.f:15.72:

      save ma,inext,inextp
                                                                        1
Error: Unexpected attribute declaration statement at (1)
make[2]: *** [/Code/neurofem-simbio-code/trunk/neurofem/lib/libsolver_linux_dbx.a(ransol.o)] Error 1
make[2]: Leaving directory `/Code/neurofem-simbio-code/trunk/toolbox/linearalgebra/libsol'
make[1]: *** [libsolver] Error 2
make[1]: Leaving directory `/Code/neurofem-simbio-code/trunk/neurofem/lib'
making all in /Code/neurofem-simbio-code/trunk/lib...
make[1]: Entering directory `/Code/neurofem-simbio-code/trunk/lib'
#anweightereloretaeeg_c.o anweightereloretameg_c.o
ar -rv libvista_linux_dbx.a FIL_Vista_Attr.o FIL_Vista_Basic.o FIL_Vista_File.o FIL_Vista_Graph.o FIL_Vista_Image.o
r - FIL_Vista_Attr.o
r - FIL_Vista_Basic.o
r - FIL_Vista_File.o
r - FIL_Vista_Graph.o
r - FIL_Vista_Image.o
ar -s libvista_linux_dbx.a
ar -rv libinverse_linux_dbx.a *.o
r - CON_AbstractPersistenceArchive_i.o
r - Error.o
r - FIL_Fiff_c.o
r - FIL_IOEngine_c.o
a - FIL_Vista_Attr.o
a - FIL_Vista_Basic.o
a - FIL_Vista_File.o
a - FIL_Vista_Graph.o
a - FIL_Vista_Image.o
r - GRI_GridGeneratorFif_c.o
r - INV_AnalyzerInverseLinearFocuss_c.o
r - INV_AnalyzerSpatioTemporalInverse_c.o
r - INV_D1Mach.o
r - IP_BRE_AbstractCriteria_c.o
r - IP_BRE_CriteriaMinimumSquareError_c.o
r - IP_ERR_AbstractErrorEstimator_c.o
r - IP_ERR_AbstractSourceSimilarityMetric_c.o
r - IP_ERR_ErrorEstimatorAllSimulatorParameters_c.o
r - IP_ERR_SourcePosDirMagSimilarityMetric_c.o
r - IP_GOA_AbstractGoalFunctionEEGMEG_c.o
r - IP_GOA_AbstractGoalFunction_c.o
r - IP_GOA_GoalFunctionDipoleFixed_c.o
r - IP_GOA_GoalFunctionDipoleRotating_c.o
r - IP_GOA_GoalFunctionFitSphere_c.o
r - IP_GRI_AbstractGridGenerator_c.o
r - IP_GRI_AbstractSourceParameterGenerator_c.o
r - IP_GRI_GridGeneratorAsa_c.o
r - IP_GRI_GridGeneratorPassedData_c.o
r - IP_GRI_GridGeneratorSingleDipoles_c.o
r - IP_GRI_GridGeneratorSurfaceSphere_c.o
r - IP_GRI_GridGeneratorVolumeSphere_c.o
r - IP_GRI_SourceParameterGeneratorInSearchvolume_c.o
r - IP_INI_AbstractInitialGuess_c.o
r - IP_INI_InitialGuessBestOfGrid_c.o
r - IP_INI_InitialGuessStandard_c.o
r - IP_INV_AbstractAnalyzerInverseContinuous_c.o
r - IP_INV_AbstractAnalyzerInverseDiscreteScan_c.o
r - IP_INV_AbstractAnalyzerInverseDiscrete_c.o
r - IP_INV_AbstractAnalyzerInverse_c.o
r - IP_INV_AbstractAnalyzer_c.o
r - IP_INV_AnalyzerInverseDipoleFit_c.o
r - IP_INV_AnalyzerInverseGoalFunctionScan_c.o
r - IP_INV_AnalyzerInverseLinear_c.o
r - IP_INV_AnalyzerInverseMusic_c.o
r - IP_OPT_AbstractOptimizerContinuous_c.o
r - IP_OPT_AbstractOptimizer_c.o
r - IP_OPT_OptimizerMarquardt_c.o
r - IP_OPT_OptimizerSimplex_c.o
r - IP_REG_AbstractRegularizer_c.o
r - IP_REG_RegularizerCovariance_c.o
r - IP_REG_RegularizerTikhonov_c.o
r - IP_REG_RegularizerTruncSVD_c.o
r - IP_SEA_AbstractSearchVolumeWithBoundaries_c.o
r - IP_SEA_AbstractSearchVolume_c.o
r - IP_SEA_SearchVolumeInfinite_c.o
r - IP_SEA_SearchVolumeSphere_c.o
r - IP_SEA_SearchVolumeWithBoundariesSpheres_c.o
r - IP_SIG_AbstractAnalyzerTransformInvertible_c.o
r - IP_SIG_AbstractAnalyzerTransform_c.o
r - IP_SIG_AbstractDatahandler_c.o
r - IP_SIG_AbstractLaplaceOperatorElementCalculator_c.o
r - IP_SIG_AnalyzerAverager_c.o
r - IP_SIG_AnalyzerMEGConvert_c.o
r - IP_SIG_LaplaceOperatorElementCalculatorRegular3D_c.o
r - IP_SIM_AbstractSimulatorEEGMEG_c.o
r - IP_SIM_AbstractSimulator_c.o
r - IP_SIM_AnalyzerMagSystemMatrixComputation_c.o
r - IP_SIM_AnalyzerSystemMatrixComputation_c.o
r - IP_SIM_ParameterSimulator_c.o
r - IP_SIM_SensorConfiguration_c.o
r - IP_SIM_SimulatorEEGBEM_c.o
r - IP_SIM_SimulatorEEGPrecomputedLeadfieldMatrix_c.o
r - IP_SIM_SimulatorEEGSpheres_c.o
r - IP_SIM_SimulatorMEGBEM_c.o
r - IP_SIM_SimulatorMEGSpheres_c.o
r - IP_STA_AbstractAnalyzerStatistic_c.o
r - IP_STA_AnalyzerStatisticMomentsOneRandomVariable_c.o
r - IP_WEI_AbstractWeighter_c.o
r - IP_WEI_UnaryWeighter_c.o
r - IP_WEI_WeighterLeadfieldNormalization_c.o
r - IP_WEI_WeighterLoreta_c.o
r - IP_WEI_WeighterSourceCovariance_c.o
r - LIN_Auxil.o
r - OPT_OptimizerSimplex_c.o
r - SIG_AbstractDatawindow_c.o
r - SIG_DataWindowBartlett_c.o
r - SIG_DataWindowCosinus_c.o
r - SIG_DataWindowSquare_c.o
r - SIG_DataWindowWelch_c.o
r - WEI_AbstractLaplaceOperator_c.o
r - WEI_LaplaceOperator2D_c.o
r - WEI_LaplaceOperatorRegular3D_c.o
r - WEI_WeighterLoretaEEG_c.o
r - WEI_WeighterLoretaMEG_c.o
r - WEI_WeighterResolutionKernelPartial_c.o
r - WEI_WeighterSLoretaEEG_c.o
r - WEI_WeighterSLoretaMEG_c.o
r - toms705.o
ar -d libinverse_linux_dbx.a FIL_Vista_Attr.o FIL_Vista_Basic.o FIL_Vista_File.o FIL_Vista_Graph.o FIL_Vista_Image.o
ar -s libinverse_linux_dbx.a
make[1]: Leaving directory `/Code/neurofem-simbio-code/trunk/lib'
making all in /Code/neurofem-simbio-code/trunk/inverse...
make[1]: Entering directory `/Code/neurofem-simbio-code/trunk/inverse'
ar -rv libnewinverse_linux_dbx.a *.o
ar: creating libnewinverse_linux_dbx.a
a - CON_MatrixHeader_c.o
a - DAT_IndexInterval_c.o
a - DAT_RegGrid3dHeader_c.o
a - FIL_ChannelListWrapper_c.o
a - FIL_ChannelList_c.o
a - FIL_RefDataReaderApp_c.o
a - FIL_RefDataReaderMultiFileAsa_c.o
a - FIL_RefDataReader_c.o
a - GOA_AbstractGoalfunctionEEGMEGCondFit_c.o
a - GOA_GoalFunctionDipoleRotatingCondFit_c.o
a - INV_AnalyzerInverseConductivityFitting_c.o
a - INV_AnalyzerInverseSAM_c.o
a - INV_AnalyzerInverseSimulatedAnnealing_c.o
a - INV_BeamfEstimateDipDir_c.o
a - INV_DataCovParams_c.o
a - INV_DataCov_c.o
a - INV_LinearEstimationCondFit_c.o
a - INV_SamParams_c.o
a - INV_ScalarBeamfCoeffs_c.o
a - INV_SingleLeadFieldManager_c.o
a - INV_VecBeamfCoeffs_c.o
a - SIM_SimulatorEEGPrecomputedLeadfieldMatrixCondFit_c.o
a - STA_RndNumGen_c.o
a - UTI_ByteOrder_c.o
a - UTI_DebugFuncs_c.o
a - UTI_MatrixCalc_c.o
a - ananalyzerinversebeamformer_c.o
a - ananalyzerinversedatacov_c.o
ar -s libnewinverse_linux_dbx.a
mv libnewinverse_linux_dbx.a ../lib
make[1]: Leaving directory `/Code/neurofem-simbio-code/trunk/inverse'
making all in /Code/neurofem-simbio-code/trunk/uif...
make[1]: Entering directory `/Code/neurofem-simbio-code/trunk/uif'
debug2: channel 0: window 999408 sent adjust 49168
mpiCC -g -pedantic ../application/uif/uif1_c.cpp -c -o uif1_c.o -I../toolbox/linearalgebra/pebbles/pebbles/  -I../ipm_toolbox/inverse/ -I../ipm_toolbox/statistics/ -I../ipm_toolbox/signalproc/ -I../ipm_toolbox/breakcriteria/ -I../toolbox/signalproc/ -I../ipm_toolbox/errorest/ -I../ipm_toolbox/goalfunctions/ -I../ipm_toolbox/grid/ -I../ipm_toolbox/initialguess/ -I../toolbox/weighter/ -I../ipm_toolbox/optimizer/ -I../ipm_toolbox/regularizer/ -I../ipm_toolbox/searchvolume/ -I../ipm_toolbox/simulator/ -I../ipm_toolbox/weighter/ -I../toolbox/ -I../toolbox/inverse/ -I../ipm_toolbox/simulator/bem/ -I../toolbox/grid/ -I../ipm_toolbox/optimizer/marquardt/ -I../ipm_toolbox/optimizer/simplex/ -I../toolbox/optimizer/simplex/ -I../ipm_toolbox/simulator/analytic/ -I../misc/ -I../converters/RES4toNeuroFEM/ -I../converters/RES4toNeuroFEM/ByteSwap/ -I../converters/RES4toNeuroFEM/ReadRES4/ -I../converters/RES4toNeuroFEM/Sensor/ -I../converters/RES4toNeuroFEM/Sensortype/ -I../converters/RES4toNeuroFEM/System/ -I../converters/RES4toNeuroFEM/System/include/ -I../toolbox/goalfunctions/ -I../inverse/ -I../toolbox/inverse/beamf/ -I../toolbox/statistics/ -I../toolbox/simulator/fem/ -I../toolbox/utilities/ -I../toolbox/fileio/ -I../toolbox/datatypes/ -I../toolbox/container/ -I../neurofem/converters/gmv_to_geoknw/ -I../neurofem/converters/img2mesh/ -I../misc/neurofem/colsamm/ -I../misc/neurofem/ -I../application/uif/ -I../toolbox/linearalgebra/ -I../toolbox/fileio/vista/ -ansi -D SER_PEBBLES_SOLVER -I../toolbox/linearalgebra/pebbles/libsrc
In file included from /usr/include/c++/4.6/backward/strstream:52:0,
                 from ../toolbox/linearalgebra/pebbles/libsrc/prepro/poutback.hh:39,
                 from ../toolbox/linearalgebra/pebbles/pebbles/pebbles.hh:52,
                 from ../toolbox/simulator/fem/SIM_SimulatorEEGMEGNeuroFEMPebbles_c.h:52,
                 from ../application/uif/uif1_c.h:152,
                 from ../application/uif/uif1_c.cpp:73:
/usr/include/c++/4.6/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
In file included from ../misc/neurofem/NeuroFEM.h:73:0,
                 from ../application/uif/uif1_c.h:148,
                 from ../application/uif/uif1_c.cpp:73:
/usr/include/g2c.h:131:14: error: ‘typedef long int Long’ redeclared as different kind of symbol
../toolbox/fileio/FIL_IOEngine_c.h:100:26: error: previous declaration of ‘AllocType Long’
In file included from ../application/uif/uif1_c.h:74:0,
                 from ../application/uif/uif1_c.cpp:73:
../toolbox/container/CON_FileMatrix_t.h: In member function ‘void CON_FileMatrix_t<T>::setFilename(std::string) [with T = double, std::string = std::basic_string<char>]’:
../application/uif/uif1_c.cpp:574:49:   instantiated from here
../toolbox/container/CON_FileMatrix_t.h:256:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat]
../toolbox/container/CON_FileMatrix_t.h: In constructor ‘CON_FileMatrix_t<T>::CON_FileMatrix_t(std::string) [with T = double, std::string = std::basic_string<char>]’:
../application/uif/uif1_c.cpp:1152:69:   instantiated from here
../toolbox/container/CON_FileMatrix_t.h:72:3: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[1024]’ [-Wformat]
make[1]: *** [uif1_c.o] Error 1
make[1]: Leaving directory `/Code/neurofem-simbio-code/trunk/uif'
make: *** [Subtraction] Error 2

Building from the clean SVN version also fails. I have all the symbolic links in place as required and as far as I can tell I have the dependencies. On OSX other things fail, but I'd rather have Ubuntu working first.

Any advice would be very helpful. Which operating system is this meant to be run on? Perhaps I can spin up a VM or AWS instance to get the benchmark values I need.

Thanks,

Erik

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