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

Wed Apr 16 17:39:24 EDT 2014

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
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/cgi-bin/mailman/listinfo/community
>