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

Thu Apr 24 07:36:54 EDT 2014

Hi!
First of all - the problem disappears in itk 4.5.2.
I am still confused:
- is it enough to set -DITKV3_COMPATIBILITY= true
- only set -DModule_ITKIOMINC=ON
- have them both

None of the authors of our project can now spend time on compatibility
issues. We will address  in a near future.

Thanks
Anka

On Wed, Apr 23, 2014 at 11:06 PM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Anka,
>
> It may be easier to resolve any compatibility issues -- why is ITKv3
> compatibility turned on?
>
> Thanks,
> Matt
>
> On Wed, Apr 16, 2014 at 6:18 PM, Anka Kochanowska
> <anka at bic.mni.mcgill.ca> wrote:
> > 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
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Community mailing list
> >> > Community at itk.org
> >> > http://public.kitware.com/cgi-bin/mailman/listinfo/community
> >> >
> >
> >
>
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