Comments (8)
dakcarto
commented on June 15, 2024
Hi Martina,
Please provide logs, i.e. brew gist-logs --config --doctor orfeo-40. See Homebrew Troubleshooting.
from homebrew-osgeo4mac.
Mporfiri
commented on June 15, 2024
Hi Larry,
find the logs at the following link:
https://gist.github.com/b089a7321598fce40105
Thank you for you interest and time, let me know if you need more information.
Regards,
Martina
from homebrew-osgeo4mac.
dakcarto
commented on June 15, 2024
The error is related to your GDAL install:
[ 89%] Building CXX object Code/Learning/CMakeFiles/OTBLearning.dir/otbNonGaussianRBFKernelFunctor.cxx.o
cd /tmp/orfeo-40-5289/OTB-4.0.0/build/Code/Learning && /usr/local/Library/ENV/4.3/clang++ -DOTBLearning_EXPORTS -DOTB_USE_INTERNAL_OPENTHREADS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_XML_LIB -fPIC -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbopenthreads/OpenThreads/include -isystem /usr/local/Cellar/qt/4.8.6/include -F/usr/local/Cellar/qt/4.8.6/lib -isystem /usr/local/Cellar/qt/4.8.6/include/QtGui -isystem /usr/local/Cellar/qt/4.8.6/include/QtXml -isystem /usr/local/Cellar/qt/4.8.6/lib/QtCore.framework/Headers -I/tmp/orfeo-40-5289/OTB-4.0.0/build -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/BasicFilters -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/ContrastEnhancement -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/ChangeDetection -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Common -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/DisparityMap -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/FeatureExtraction -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Fusion -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Fuzzy -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/GeospatialAnalysis -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Hyperspectral -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/IO -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Learning -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Markov -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/MultiScale -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/MultiTemporal -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/OBIA -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/ObjectDetection -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Projections -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Radiometry -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/SARPolarimetry -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Segmentation -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Simulation -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/SpatialReasoning -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Testing -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/CurlAdapters -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/OssimAdapters -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/TinyXMLAdapters -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/OGRAdapters -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/ITKPendingPatches -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/ApplicationEngine -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbsvm -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbossimplugins -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbossimplugins/ossim -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/InsightJournal -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otb6S -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbedison/segm -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbedison/prompt -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbedison/edge -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbconfigfile -I/tmp/orfeo-40-5289/OTB-4.0.0/Code/Wrappers/QtWidget -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/BGL -I/Library/Frameworks/gdal.framework/Headers -I/usr/local/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/otbsiftfast -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/DoubleConversion/src/double-conversion -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/KWSys/src -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/VNL/src/vxl/vcl -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/VNL/src/vxl/core -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/VNL/src/vxl/vcl -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/VNL/src/vxl/core -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/VNLInstantiation/include -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/Core/Common -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/Common/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/FiniteDifference/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageFilterBase/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/CurvatureFlow/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/ImageAdaptors/include -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/Netlib -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/Statistics/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/Transform/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/ImageFunction/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageGrid/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/AnisotropicSmoothing/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageCompose/include -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/IO/ImageBase -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/IO/ImageBase/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/Mesh/include -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/ZLIB/src -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/ZLIB/src -I/tmp/orfeo-40-5289/OTB-4.0.0/build/Utilities/ITK/Modules/ThirdParty/MetaIO/src/MetaIO -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/ThirdParty/MetaIO/src/MetaIO -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/SpatialObjects/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageStatistics/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Path/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageIntensity/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageLabel/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Thresholding/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/ConnectedComponents/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/MathematicalMorphology/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/LabelMap/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/BinaryMathematicalMorphology/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/NarrowBand/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/DistanceMap/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/QuadEdgeMesh/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/FastMarching/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageCompare/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Smoothing/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageGradient/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageSources/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageFeature/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/Optimizers/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/SignedDistanceFunction/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/LevelSets/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/AntiAlias/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/Polynomials/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/BiasCorrection/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/Classifiers/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Colormap/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/FFT/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Convolution/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Deconvolution/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/DeformableMesh/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/Denoising/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/DisplacementField/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/Eigen/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/GPUCommon/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Core/GPUFiniteDifference/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/GPUAnisotropicSmoothing/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/GPUImageFilterBase/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Registration/GPUCommon/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Registration/Common/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Registration/PDEDeformable/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Registration/GPUPDEDeformable/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/GPUSmoothing/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/GPUThresholding/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/ImageFusion/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/KLMRegionGrowing/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/LabelVoting/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/LevelSetsv4/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/MarkovRandomFieldsClassifiers/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/Optimizersv4/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Registration/Metricsv4/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Numerics/NeuralNetworks/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/QuadEdgeMeshFiltering/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/RegionGrowing/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Registration/RegistrationMethodsv4/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Filtering/SpatialFunction/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/Voronoi/include -I/tmp/orfeo-40-5289/OTB-4.0.0/Utilities/ITK/Modules/Segmentation/Watersheds/include -o CMakeFiles/OTBLearning.dir/otbNonGaussianRBFKernelFunctor.cxx.o -c /tmp/orfeo-40-5289/OTB-4.0.0/Code/Learning/otbNonGaussianRBFKernelFunctor.cxx
/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/OGRAdapters/otbOGRDataSourceWrapper.cxx:129:17: error: no member named 'SetDriver' in 'OGRDataSource'; did you mean 'GetDriver'?
m_DataSource->SetDriver(d);
^~~~~~~~~
GetDriver
/Library/Frameworks/gdal.framework/Headers/ogrsf_frmts.h:234:25: note: 'GetDriver' declared here
OGRSFDriver *GetDriver() const;
^
/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/OGRAdapters/otbOGRDataSourceWrapper.cxx:129:27: error: too many arguments to function call, expected 0, have 1
m_DataSource->SetDriver(d);
~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/gdal.framework/Headers/ogrsf_frmts.h:234:5: note: 'GetDriver' declared here
OGRSFDriver *GetDriver() const;
^
/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/OGRAdapters/otbOGRDataSourceWrapper.cxx:175:13: error: no member named 'SetDriver' in 'OGRDataSource'; did you mean 'GetDriver'?
source->SetDriver(d);
^~~~~~~~~
GetDriver
/Library/Frameworks/gdal.framework/Headers/ogrsf_frmts.h:234:25: note: 'GetDriver' declared here
OGRSFDriver *GetDriver() const;
^
/tmp/orfeo-40-5289/OTB-4.0.0/Code/UtilitiesAdapters/OGRAdapters/otbOGRDataSourceWrapper.cxx:175:23: error: too many arguments to function call, expected 0, have 1
source->SetDriver(d);
~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/gdal.framework/Headers/ogrsf_frmts.h:234:5: note: 'GetDriver' declared here
OGRSFDriver *GetDriver() const;
^
4 errors generated.
make[2]: *** [Code/UtilitiesAdapters/OGRAdapters/CMakeFiles/OTBOGRAdapters.dir/otbOGRDataSourceWrapper.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
brew doctor indicates you have 'unbrewed' libraries and components for GDAL in /usr/local/lib. There is also a CMake reference to /Library/Frameworks/gdal.framework, which is not the Kyngchaos.com GDAL.framework; so, I can only infer that you have manually compiled/installed GDAL in the past.
This probably caused Homebrew's gdal formula to fail to link into HOMEBREW_PREFIX, i.e. /usr/local in your case, when it was installed.
Given the brew doctor output you should:
-
Uninstall the manually built GDAL (ideally, find the source build directory you installed from and run
make uninstall; otherwise, you will need to do it manually) -
Do
brew link gdal(gdalshould be already built in/usr/local/Cellar/gdal/1.11.0, but is probably not linked) -
Run
brew doctoragain and fix everything noted there, e.g. probably:Warning: You have uncommitted modifications to Homebrew If this a surprise to you, then you should stash these modifications. Stashing returns Homebrew to a pristine state but can be undone should you later need to do so for some reason. cd /usr/local/Library && git stash && git clean -d -f Warning: /usr/bin occurs before /usr/local/bin This means that system-provided programs will be used instead of those provided by Homebrew. The following tools exist at both paths: c++ cpp g++ gcc gcov Consider setting your PATH so that /usr/local/bin occurs before /usr/bin. Here is a one-liner: echo export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile Warning: Your Xcode (5.0.2) is outdated Please update to Xcode 5.1.1. Xcode can be updated from the App Store. -
Retry installing OTB 4.0 with
brew install orfeo-40 -dv, which will output debug info and offer some other options when hitting an error.
Note: This may be an incompatibility with GDAL 1.11.0. I will also recompile here to double-check that.
from homebrew-osgeo4mac.
dakcarto
commented on June 15, 2024
Tested here, builds fine on OS X 10.7.5 against GDAL 1.11.
from homebrew-osgeo4mac.
Mporfiri
commented on June 15, 2024
Hi Lerry,
following your suggestion I have successfully compiled OTB 4.0.
Unfortunately I have a problem doing the executable (the simplest one, print 'Hello world'). I do not know if this is the right place where post my issue. However, trying to run the executable I get the following error:
dyld: Symbol not found: _json_tokener_errors
Referenced from: /usr/local/opt/liblwgeom/lib/liblwgeom-2.1.1.dylib
Expected in: /usr/local/lib/libjson-c.2.dylib
in /usr/local/opt/liblwgeom/lib/liblwgeom-2.1.1.dylib
Trace/BPT trap: 5
I have already installed json-c-0.11 library.
Thank you very much for your time, feel free to close this issue if you want.
Regards,
Martina
from homebrew-osgeo4mac.
dakcarto
commented on June 15, 2024
See: Homebrew/legacy-homebrew#29430. You may have installed some packages before json-c was reverted to 0.11.
Try the following:
brew info json-cand verify that 0.11 is the version you have linked (noted by asterisks at end)- If
/usr/local/Cellar/json-c/0.12exists, remove it brew reinstall $(brew uses json-c --installed)which will reinstallliblwgeomandpostgis(if installed)
You do not have to recompile orfeo-40, since it is only a dylib issue with a dependency.
from homebrew-osgeo4mac.
dakcarto
commented on June 15, 2024
See also: #33 (comment)
from homebrew-osgeo4mac.
Mporfiri
commented on June 15, 2024
Hi Larry,
following your suggestion I fixed my problem and the executable runs.
Thank you very much!!
Martina
from homebrew-osgeo4mac.
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