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[Seg3D] Re: Re: ubuntu 11.10 build error in Seg3D_1.12_20090930

Chronological Thread 
  • From: Ramón Casero Cañas <>
  • To:
  • Subject: [Seg3D] Re: Re: ubuntu 11.10 build error in Seg3D_1.12_20090930
  • Date: Thu, 16 Feb 2012 12:40:27 +0000

On 25/01/12 03:50, Ayla Khan wrote:
Hi Ramon,

We are not building the wxWidgets interface any more, but I remember
that we ran into similar problems with wxWidgets GTK 2.8.10. We patched
it for building on Linux - the source is still available:
if you want to have a look at it. If I recall correctly, we were
compiling with GCC 4.5.

Hi Ayla,

I have been trying this for the last week, using gcc 4.5, fresh check out, and fixes here and there, but it just doesn't want to compile.

A colleague is working on segmentation of fetuses arms, and they would like to try the spline tool (they do a lot of segmentations at the hospital, and this could speed them up). AFAIK, the only implementation available is in

as it was never merged back into trunk or ported to Seg3D2. Doing a checkout, and running

$ ./ --seg3d-only

gives a couple of compilation errors that can be fixed by editing src/Externals/vispack/CMakeLists.txt from




and also adding #include <stdio.h> to src/Externals/vispack/apps/distance/IOScalarField.h and src/Externals/vispack/apps/distance/ReconstructionField.cxx.

However, now I get a linking error (see at the bottom). I suspect, this is because external libraries changed, while the code in the branch remained fixed. Is there a way to checkout the source code of the externals as they were when my branch was last compilable?

On a related note, is there any actual plan to add the spline tool into Seg3D2, or is this something we should better consider a thing of the past (2 years after our visit to SCI ;) ) and just move on?

Linking CXX executable ../../../../distance3
CMakeFiles/distance3.dir/volutils.o: In function `writeTensorVolumeFile(char*, VISVolume<VISMatrix> const&)':
volutils.cxx:(.text+0x44f): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x47e): undefined reference to `nrrdAlloc_va'
volutils.cxx:(.text+0x5b5): undefined reference to `nrrdSave'
volutils.cxx:(.text+0x5c4): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0x5c9): undefined reference to `biffGetDone'
volutils.cxx:(.text+0x64a): undefined reference to `nrrdNuke'
CMakeFiles/distance3.dir/volutils.o: In function `writeTensorVolumeFile(char*, VISVolume<VISMatrix> const&, VISVolume<float> const&)':
volutils.cxx:(.text+0x6d3): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x704): undefined reference to `nrrdAlloc_va'
volutils.cxx:(.text+0x857): undefined reference to `nrrdSave'
volutils.cxx:(.text+0x866): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0x86b): undefined reference to `biffGetDone'
volutils.cxx:(.text+0x8ec): undefined reference to `nrrdNuke'
CMakeFiles/distance3.dir/volutils.o: In function `readScalarVolumeFile(char*)':
volutils.cxx:(.text+0x9de): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x9ee): undefined reference to `nrrdLoad'
volutils.cxx:(.text+0xa16): undefined reference to `nrrdType'
volutils.cxx:(.text+0xa1b): undefined reference to `airEnumStr'
volutils.cxx:(.text+0xae3): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0xae8): undefined reference to `biffGetDone'
CMakeFiles/distance3.dir/volutils.o: In function `writeVectorVolumeFile(char*, VISVolume<VISVector> const&)':
volutils.cxx:(.text+0x111f): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x114e): undefined reference to `nrrdAlloc_va'
volutils.cxx:(.text+0x1215): undefined reference to `nrrdSave'
volutils.cxx:(.text+0x1224): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0x1229): undefined reference to `biffGetDone'
volutils.cxx:(.text+0x12aa): undefined reference to `nrrdNuke'
CMakeFiles/distance3.dir/volutils.o: In function `writeScalarVolumeFile(char*, VISVolume<float> const&)':
volutils.cxx:(.text+0x1324): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x1343): undefined reference to `nrrdAlloc_va'
volutils.cxx:(.text+0x13bc): undefined reference to `nrrdSave'
volutils.cxx:(.text+0x13c8): undefined reference to `nrrdNuke'
volutils.cxx:(.text+0x13f3): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0x13f8): undefined reference to `biffGetDone'
CMakeFiles/distance3.dir/volutils.o: In function `readTensorVolumeFile(char*)':
volutils.cxx:(.text+0x1484): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x1496): undefined reference to `nrrdLoad'
volutils.cxx:(.text+0x14d0): undefined reference to `nrrdType'
volutils.cxx:(.text+0x14d5): undefined reference to `airEnumStr'
volutils.cxx:(.text+0x159d): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0x15a2): undefined reference to `biffGetDone'
volutils.cxx:(.text+0x165e): undefined reference to `nrrdType'
volutils.cxx:(.text+0x1663): undefined reference to `airEnumStr'
volutils.cxx:(.text+0x1695): undefined reference to `nrrdElementSize'
volutils.cxx:(.text+0x16a2): undefined reference to `nrrdElementNumber'
volutils.cxx:(.text+0x1a71): undefined reference to `nrrdNuke'
CMakeFiles/distance3.dir/volutils.o: In function `readVectorVolumeFile(char*)':
volutils.cxx:(.text+0x1fd4): undefined reference to `nrrdNew'
volutils.cxx:(.text+0x1fe4): undefined reference to `nrrdLoad'
volutils.cxx:(.text+0x2016): undefined reference to `nrrdType'
volutils.cxx:(.text+0x201b): undefined reference to `airEnumStr'
volutils.cxx:(.text+0x20e9): undefined reference to `nrrdBiffKey'
volutils.cxx:(.text+0x20ee): undefined reference to `biffGetDone'
volutils.cxx:(.text+0x216b): undefined reference to `nrrdType'
volutils.cxx:(.text+0x2170): undefined reference to `airEnumStr'
volutils.cxx:(.text+0x219b): undefined reference to `nrrdElementSize'
volutils.cxx:(.text+0x21a6): undefined reference to `nrrdElementNumber'
collect2: ld returned 1 exit status
make[2]: *** [distance3] Error 1
make[1]: *** [Externals/vispack/apps/distance/CMakeFiles/distance3.dir/all] Error 2
make: *** [all] Error 2

Best regards,


Dr. Ramón Casero Cañas

Computational Biology
Department of Computer Science
University of Oxford
Wolfson Building, Parks Rd
Oxford OX1 3QD

tlf     +44 (0) 1865 610737

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