[Paraview] Linking error on MacOS X Lion
Antonio LaTorre
atorre at fi.upm.es
Thu Mar 8 10:48:32 EST 2012
Hi,
1. libvtkhdf5.dylib compiles without errors nor warnings.
2. VTK_USE_SYSTEM_HDF5 is Off in my config.
3. Same result: linking error of libvtkPVVTKExtensions.dylib
4. I already had HDF5 installed via Macports (version 1.8.8). Turning
VTK_USE_SYSTEM_HDF5 On with the Macports HDF5 library
configures ok (cmake finds the include dirs and the libs) but it fails
to compile with the following error:
[ 30%] Building CXX object Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o
In file included from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:29,
from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.h:28,
from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:30:22: error: H5public.h: No such file or directory
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:36:18: error: hdf5.h: No such file or directory
In file included from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:29,
from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.h:28,
from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:42: error: 'hid_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:43: warning: 'HDF5TypeToXdmfType' initialized and declared 'extern'
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:43: error: 'hid_t' was not declared in this scope
In file included from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.h:28,
from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:93: error: 'hid_t' has not been declared
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:94: error: 'hid_t' has not been declared
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:163: error: 'hid_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:165: error: 'hid_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:218: error: 'hid_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:219: error: 'hid_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:234: error: 'hssize_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:236: error: 'hsize_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:237: error: 'hsize_t' does not name a type
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h: In member function 'XdmfInt32 XdmfDataDesc::CopyType(XdmfDataDesc*)':
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:89: error: 'class XdmfDataDesc' has no member named 'GetDataType'
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h: In member function 'XdmfInt64 XdmfDataDesc::GetStart(XdmfInt64)':
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:151: error: 'class XdmfDataDesc' has no member named 'Start'
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h: In member function 'XdmfInt64 XdmfDataDesc::GetStride(XdmfInt64)':
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:153: error: 'class XdmfDataDesc' has no member named 'Stride'
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h: In member function 'XdmfInt64 XdmfDataDesc::GetCount(XdmfInt64)':
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:155: error: 'class XdmfDataDesc' has no member named 'Count'
In file included from /usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.h: At global scope:
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.h:90: error: 'hid_t' has not been declared
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:384: error: 'XdmfInt32 XdmfArray::CopyShape' is not a static member of 'class XdmfArray'
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:384: error: 'hid_t' was not declared in this scope
/usr/local/src/ParaView-3.12.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:384: error: expected ',' or ';' before '{' token
make[2]: *** [Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o] Error 1
make[1]: *** [Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/all] Error 2
make: *** [all] Error 2
5. Bug reported: http://paraview.org/Bug/view.php?id=12982
Thanks for your quick response.
Regards,
Antonio
——
Antonio LaTorre
CeSViMa - Universidad Politécnica de Madrid
Phone: +34 91 452 49 00 ext. 1762
Fax: +34 91 336 73 73
e-mail: atorre at fi.upm.es (mailto:atorre at fi.upm.es)
http://laurel.datsi.fi.upm.es/~atorre
CeSViMa - Parque Tecnológico UPM
Campus de Montegancedo
28223, Pozuelo de Alarcón, Madrid
España
On Thursday, March 8, 2012 at 2:55 PM, David E DeMarle wrote:
> It's likely that turning on VTK_USE_BOOST brings in code (like the Enzo and Flash readers) that need features from hdf5 that we don't compile.
>
> This is likely a bug. Can you help us resolve it by:
>
> 1) Were there any hdf5 related compilation errors or warnings for you?
> 2) What is your setting of VTK_USE_SYSTEM_HDF5?
> 3) Try recompiling with VTK_USE_BOOST off.
> 4) Try turning VTK_USE_SYSTEM_HDF5 on and point it to a recent HDF5.
>
> 5) File a bug report.
>
>
> thanks,
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
>
> On Wed, Mar 7, 2012 at 11:22 AM, Antonio LaTorre <atorre at fi.upm.es (mailto:atorre at fi.upm.es)> wrote:
> > >
> > > I'm completely new to Paraview, but it seems that it is not finding the symbols related to HDF5
> > > when it tries to link the lib. Should I configure something on the CMakeCache to make it find the
> > > lib with those symbols? Is it a bug of the compilation process?
> > >
> > > FYI, I only changed a couple of vars in CMake: BUILD_SHARED_LIBS = ON and VTK_USE_BOOST = ON.
> > >
> > > I'm on MacOS X 10.7 and use Apple's Clang distributed with the latest version of Xcode.
> > >
> > > Regards and thanks in advance for your help.
> >
> >
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