<div dir="ltr">Hi!<div>First of all - the problem disappears in itk 4.5.2.</div><div>I am still confused:</div><div>- is it enough to set -DITKV3_COMPATIBILITY= true</div><div>- only set -DModule_ITKIOMINC=ON</div><div>- have them both  </div>
<div><br></div><div>None of the authors of our project can now spend time on compatibility issues. We will address  in a near future.</div><div><br></div><div>Thanks </div><div>Anka</div><div><br></div><div><br></div><div>
 </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Apr 23, 2014 at 11:06 PM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Anka,<br>
<br>
It may be easier to resolve any compatibility issues -- why is ITKv3<br>
compatibility turned on?<br>
<br>
Thanks,<br>
Matt<br>
<br>
On Wed, Apr 16, 2014 at 6:18 PM, Anka Kochanowska<br>
<div class="HOEnZb"><div class="h5"><<a href="mailto:anka@bic.mni.mcgill.ca">anka@bic.mni.mcgill.ca</a>> wrote:<br>
> Thanks Matt!<br>
> I am using all systems embedded.<br>
><br>
> Anka<br>
><br>
><br>
><br>
><br>
> On Wed, Apr 16, 2014 at 5:39 PM, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
> wrote:<br>
>><br>
>> Hi Anka,<br>
>><br>
>> Are you using a system HDF5?  The embedded one may work better.<br>
>><br>
>> Thanks,<br>
>> Matt<br>
>><br>
>> On Wed, Apr 16, 2014 at 2:02 PM, Anka Kochanowska<br>
>> <<a href="mailto:anka@bic.mni.mcgill.ca">anka@bic.mni.mcgill.ca</a>> wrote:<br>
>> > Hi!<br>
>> > I am using Module_ITKIOMINC in my project. When I do not include<br>
>> > Module_ITKV3Compatibility everything works fine.<br>
>> > Unfortunately, some parts of my project are using functions from both<br>
>> > modules.<br>
>> ><br>
>> > When I build the project with both modules, I am getting linker errors.<br>
>> > It<br>
>> > seems that HDF5 is not linked in.<br>
>> ><br>
>> > I use:<br>
>> > cmake 2.8.12.2<br>
>> > itk 4,.5.1<br>
>> > gcc 4.6.3<br>
>> > Ubuntu 12.04<br>
>> ><br>
>> > Anka<br>
>> ><br>
>> > The errors are:<br>
>> ><br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(datatype.c.o):<br>
>> > In<br>
>> > function `miget_data_type_size':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/datatype.c:41:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In<br>
>> > function `milist_attr_next':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:188:<br>
>> > undefined reference to `H5Aiterate1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In<br>
>> > function `miget_attr_length':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:522:<br>
>> > undefined reference to `H5Aopen_name'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In<br>
>> > function `miget_attr_type':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:621:<br>
>> > undefined reference to `H5Aopen_name'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In<br>
>> > function `miget_attr_values':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:804:<br>
>> > undefined reference to `H5Aopen_name'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(grpattr.c.o): In<br>
>> > function `miset_attr_values':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:952:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/grpattr.c:963:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(hyper.c.o): In<br>
>> > function `mirw_hyperslab_raw':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/hyper.c:408:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(hyper.c.o): In<br>
>> > function `mirw_hyperslab_icv':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/hyper.c:621:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(hyper.c.o): In<br>
>> > function `mirw_hyperslab_normalized':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/hyper.c:1096:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /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:<br>
>> > more undefined references to `H5Dopen1' follow<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In<br>
>> > function `miget_attribute':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:438:<br>
>> > undefined reference to `H5Aopen_name'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In<br>
>> > function `minc_update_thumbnail':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1668:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1706:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1710:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1731:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1736:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1741:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1746:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In<br>
>> > function `create_dataset':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1951:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In<br>
>> > function `create_standard_dataset':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:1990:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(m2util.c.o): In<br>
>> > function `miget_scalar':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/m2util.c:2276:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volprops.c.o):<br>
>> > In<br>
>> > function `miselect_resolution':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volprops.c:267:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volprops.c:274:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volprops.c:280:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In<br>
>> > function `micreate_volume_image':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:292:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:346:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:346:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:360:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In<br>
>> > function `micreate_volume':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:664:<br>
>> > undefined reference to `H5Dcreate1'<br>
>> ><br>
>> > /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:<br>
>> > more undefined references to `H5Dcreate1' follow<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In<br>
>> > function `miget_volume_voxel_count':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:976:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > /export01/anka/itk4.5.1/itk4.5.1inst/lib/libitk_minc2.a(volume.c.o): In<br>
>> > function `miopen_volume':<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1314:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1348:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1390:<br>
>> > undefined reference to `H5Dopen1'<br>
>> ><br>
>> > /export01/anka/itk4.5.1/deb/Modules/ThirdParty/MINC/ITKMINC2_ExternalProject/libsrc2/volume.c:1391:<br>
>> > undefined reference to `H5Dopen1'<br>
>> > collect2: ld returned 1 exit status<br>
>> ><br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
>> > Community mailing list<br>
>> > <a href="mailto:Community@itk.org">Community@itk.org</a><br>
>> > <a href="http://public.kitware.com/cgi-bin/mailman/listinfo/community" target="_blank">http://public.kitware.com/cgi-bin/mailman/listinfo/community</a><br>
>> ><br>
><br>
><br>
</div></div></blockquote></div><br></div>