[ITK] ITKV3 Compatibility broken in itk4.5.1 when using Module_ITKIOMINC

Wed Apr 16 18:18:51 EDT 2014

Thanks Matt!
I am using all systems embedded.

Anka

On Wed, Apr 16, 2014 at 5:39 PM, Matt McCormick
<matt.mccormick at kitware.com>wrote:

> Hi Anka,
>
> Are you using a system HDF5?  The embedded one may work better.
>
> Thanks,
> Matt
>
> On Wed, Apr 16, 2014 at 2:02 PM, Anka Kochanowska
> <anka at bic.mni.mcgill.ca> wrote:
> > Hi!
> > I am using Module_ITKIOMINC in my project. When I do not include
> > Module_ITKV3Compatibility everything works fine.
> > Unfortunately, some parts of my project are using functions from both
> > modules.
> >
> > When I build the project with both modules, I am getting linker errors.
> It
> > seems that HDF5 is not linked in.
> >
> > I use:
> > cmake 2.8.12.2
> > itk 4,.5.1
> > gcc 4.6.3
> > Ubuntu 12.04
> >
> > Anka
> >
> > The errors are:
> >
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(datatype.c.o): In
> > function `miget_data_type_size':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/datatype.c:41:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In
> > function `milist_attr_next':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:188:
> > undefined reference to `H5Aiterate1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In
> > function `miget_attr_length':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:522:
> > undefined reference to `H5Aopen_name'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In
> > function `miget_attr_type':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:621:
> > undefined reference to `H5Aopen_name'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In
> > function `miget_attr_values':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:804:
> > undefined reference to `H5Aopen_name'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In
> > function `miset_attr_values':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:952:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:963:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(hyper.c.o): In
> > function `mirw_hyperslab_raw':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/hyper.c:408:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(hyper.c.o): In
> > function `mirw_hyperslab_icv':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/hyper.c:621:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(hyper.c.o): In
> > function `mirw_hyperslab_normalized':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/hyper.c:1096:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o):/export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:298:
> > more undefined references to `H5Dopen1' follow
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In
> > function `miget_attribute':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:438:
> > undefined reference to `H5Aopen_name'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In
> > function `minc_update_thumbnail':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1668:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1706:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1710:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1731:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1736:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1741:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1746:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In
> > function `create_dataset':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1951:
> > undefined reference to `H5Dcreate1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In
> > function `create_standard_dataset':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1990:
> > undefined reference to `H5Dcreate1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In
> > function `miget_scalar':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:2276:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volprops.c.o): In
> > function `miselect_resolution':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volprops.c:267:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volprops.c:274:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volprops.c:280:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In
> > function `micreate_volume_image':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:292:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:346:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:346:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:360:
> > undefined reference to `H5Dcreate1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In
> > function `micreate_volume':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:664:
> > undefined reference to `H5Dcreate1'
> >
> /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o):/export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:703:
> > more undefined references to `H5Dcreate1' follow
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In
> > function `miget_volume_voxel_count':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:976:
> > undefined reference to `H5Dopen1'
> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In
> > function `miopen_volume':
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1314:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1348:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1390:
> > undefined reference to `H5Dopen1'
> >
> /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1391:
> > undefined reference to `H5Dopen1'
> > collect2: ld returned 1 exit status
> >
> >
> >
> > _______________________________________________
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> > Community at itk.org
> > http://public.kitware.com/cgi-bin/mailman/listinfo/community
> >
>
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