[Insight-developers] SimpleITK compilation error

Sat Oct 1 08:04:33 EDT 2011

Hi Dan,

I am not really interested in C# wrappers, I have already turned it  
off ;-).

I used the default settings in which all wrappers are turned on at the  
beginning, then mono was detected.
I plan to set up a nightly build for SimpleITK on this machine, anyway.

Don't worry, there's no rush for C# on my side!
If you are interested in, I can prepare a virtual machine with the  
same settings for you. Once you get back, you can then have a look.

How does that sound?

Cheers,
Arnaud

On Oct 1, 2011, at 5:18 AM, Dan Mueller wrote:

> Hi Arnaud,
>
> I forgot to add: if you are not interested in C# wrappers, you can
> simply turn them off to help the build process.
>
> Are you specifically interested in the C# wrappers? Or was it turned
> on automatically because Mono was detected on your system?
>
> Cheers, Dan
>
> On 30 September 2011 17:00, Dan Mueller <dan.muel at gmail.com> wrote:
>> Hi Arnaud,
>>
>> Hmm. Looks like there is an issue wrapping enums for C# on debian. We
>> are using a special "enum as type" option in SWIG, which may be
>> contributing to the issue ("enum as integer" did not work for other
>> Linux flavours). I'm travelling for the next 2 weeks, so it may  
>> take a
>> while before I can set up a virtual machine to investigate...
>>
>> Cheers, Dan
>>
>> On 30 September 2011 15:45, Arnaud Gelas <arnaud_gelas at hms.harvard.edu 
>> > wrote:
>>> Here is what I get on next:
>>>
>>> [ 39%] Compiling C# library SimpleITKCSharpManaged
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/AffineTransform.cs(47,26):
>>> error CS0115: `itk.simple.AffineTransform.GetTransform(int)' is  
>>> marked as an
>>> override but no suitable method found to override
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/AffineTransform.cs(53,32):
>>> error CS0115: `itk.simple.AffineTransform.GetOptimizerScales(int)'  
>>> is marked
>>> as an override but no suitable method found to override
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/MattesMutualInformationMetric.cs(47,26):
>>> error CS0115:
>>> ` 
>>> itk 
>>> .simple.MattesMutualInformationMetric.GetMetric(itk.simple.Image)'  
>>> is
>>> marked as an override but no suitable method found to override
>>> Compilation failed: 3 error(s), 0 warnings
>>>
>>> ---
>>>
>>> Let me know if there's anything you want me to try here
>>>
>>> Best,
>>> Arnaud
>>>
>>> On 09/30/2011 09:32 AM, Arnaud Gelas wrote:
>>>
>>> My machine is a debian squeeze (64 bits)
>>> Mono (version): 2.6.7-5
>>> gcc: 4.6.1
>>>
>>> It was working fine yesterday (after removing the dependency to  
>>> curses)...
>>>
>>> ---
>>>
>>> I am giving a try on next, to check if it has not been fixed  
>>> there...
>>>
>>> On 09/30/2011 09:25 AM, Bradley Lowekamp wrote:
>>>
>>> Hello Arnaud,
>>> This error looks only related to CSharp. Dan Mueller is the CSharp  
>>> expert,
>>> hopefully he as some insight.
>>> What version of OS, and mono are you using?
>>> Thanks for let up know what's not working for you,
>>> Brad
>>> On Sep 30, 2011, at 9:17 AM, Arnaud Gelas wrote:
>>>
>>> Hi Brad,
>>>
>>> I am recompiling SimpleITK (master) this morning and I get  
>>> compilation
>>> errors (see errors below).
>>>
>>> BTW, is there a mailing list for SimpleITK where I could post such a
>>> message?
>>>
>>> Thanks,
>>> Arnaud
>>>
>>> Linking CXX shared module ../../lib/_SimpleITK.so
>>> Creating Python virtualenv
>>> Already using interpreter /usr/bin/python2.6
>>> New python executable in
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Testing/ 
>>> Installation/PythonVirtualenv/bin/python2.6
>>> Also creating executable in
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Testing/ 
>>> Installation/PythonVirtualenv/bin/python
>>> [ 56%] Built target SimpleITKUnitTestDriver
>>> Installing
>>> distribute 
>>> ....................................................................................................................................................................................done 
>>> .
>>> Installing
>>> pip.../home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(12,122):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `sitkUnknow_get'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(12,139):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.InterpolateFunctionEnum.InterpolateFunctionEnum(string,
>>> itk.simple.InterpolateFunctionEnum)' has some invalid arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(43,11):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(12,139):
>>> error CS1503: Argument `#2' cannot convert `object' expression to  
>>> type
>>> `itk.simple.InterpolateFunctionEnum'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(13,140):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `sitkNearestNeighbor_get'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(13,166):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.InterpolateFunctionEnum.InterpolateFunctionEnum(string,
>>> itk.simple.InterpolateFunctionEnum)' has some invalid arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(43,11):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(13,166):
>>> error CS1503: Argument `#2' cannot convert `object' expression to  
>>> type
>>> `itk.simple.InterpolateFunctionEnum'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(14,144):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `sitkLinearInterpolate_get'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(14,172):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.InterpolateFunctionEnum.InterpolateFunctionEnum(string,
>>> itk.simple.InterpolateFunctionEnum)' has some invalid arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(43,11):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(14,172):
>>> error CS1503: Argument `#2' cannot convert `object' expression to  
>>> type
>>> `itk.simple.InterpolateFunctionEnum'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(15,134):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `sitkWindowedSinc_get'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(15,157):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.InterpolateFunctionEnum.InterpolateFunctionEnum(string,
>>> itk.simple.InterpolateFunctionEnum)' has some invalid arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(43,11):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/InterpolateFunctionEnum.cs(15,157):
>>> error CS1503: Argument `#2' cannot convert `object' expression to  
>>> type
>>> `itk.simple.InterpolateFunctionEnum'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(17,86):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `ResampleImageFilter_SWIGUpcast'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(17,64):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.ImageFilter.ImageFilter(System.IntPtr, bool)' has some
>>> invalid arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ImageFilter.cs(18,12):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(17,64):
>>> error CS1503: Argument `#1' cannot convert `object' expression to  
>>> type
>>> `System.IntPtr'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(43,56):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `new_ResampleImageFilter'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(43,34):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.ResampleImageFilter.ResampleImageFilter(System.IntPtr,
>>> bool)' has some invalid arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(17,12):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/ResampleImageFilter.cs(43,34):
>>> error CS1503: Argument `#1' cannot convert `object' expression to  
>>> type
>>> `System.IntPtr'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SOptimizer.cs(44,47):
>>> error CS0117: `itk.simple.SimpleITKPINVOKE' does not contain a
>>> definition for `new_SOptimizer'
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SimpleITKPINVOKE.cs(14,7):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SOptimizer.cs(44,25):
>>> error CS1502: The best overloaded method match for
>>> `itk.simple.SOptimizer.SOptimizer(System.IntPtr, bool)' has some  
>>> invalid
>>> arguments
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SOptimizer.cs(18,12):
>>> (Location of the symbol related to previous error)
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Wrapping/ 
>>> CSharpSources/SOptimizer.cs(44,25):
>>> error CS1503: Argument `#1' cannot convert `object' expression to  
>>> type
>>> `System.IntPtr'
>>> Compilation failed: 21 error(s), 0 warnings
>>> make[5]: *** [Wrapping/SimpleITKCSharpManaged.dll] Error 1
>>> make[4]: *** [Wrapping/CMakeFiles/SimpleITKCSharpManaged.dir/all]  
>>> Error 2
>>> make[4]: *** Waiting for unfinished jobs....
>>> ..................done.
>>> Installing python module to the virtualenv
>>> running install
>>> running bdist_egg
>>> running egg_info
>>> writing SimpleITK.egg-info/PKG-INFO
>>> writing top-level names to SimpleITK.egg-info/top_level.txt
>>> writing dependency_links to SimpleITK.egg-info/dependency_links.txt
>>> warning: manifest_maker: standard file 'setup.py' not found
>>> reading manifest file 'SimpleITK.egg-info/SOURCES.txt'
>>> writing manifest file 'SimpleITK.egg-info/SOURCES.txt'
>>> installing library code to build/bdist.linux-x86_64/egg
>>> running install_lib
>>> running build_py
>>> creating build/bdist.linux-x86_64/egg
>>> copying build/lib.linux-x86_64-2.6/SimpleITK.py ->
>>> build/bdist.linux-x86_64/egg
>>> byte-compiling build/bdist.linux-x86_64/egg/SimpleITK.py to  
>>> SimpleITK.pyc
>>> [ 56%] Built target org_itk_simple_jar
>>> installing package data to build/bdist.linux-x86_64/egg
>>> running install_data
>>> copying /home/ajg23/GITROOT/SimpleITK/build/lib/_SimpleITK.so ->
>>> build/bdist.linux-x86_64/egg/
>>> creating build/bdist.linux-x86_64/egg/EGG-INFO
>>> copying SimpleITK.egg-info/PKG-INFO -> build/bdist.linux-x86_64/ 
>>> egg/EGG-INFO
>>> copying SimpleITK.egg-info/SOURCES.txt ->
>>> build/bdist.linux-x86_64/egg/EGG-INFO
>>> copying SimpleITK.egg-info/dependency_links.txt ->
>>> build/bdist.linux-x86_64/egg/EGG-INFO
>>> copying SimpleITK.egg-info/not-zip-safe ->
>>> build/bdist.linux-x86_64/egg/EGG-INFO
>>> copying SimpleITK.egg-info/top_level.txt ->
>>> build/bdist.linux-x86_64/egg/EGG-INFO
>>> creating 'dist/SimpleITK-0.3.0-py2.6.egg' and adding
>>> 'build/bdist.linux-x86_64/egg' to it
>>> removing 'build/bdist.linux-x86_64/egg' (and everything under it)
>>> Processing SimpleITK-0.3.0-py2.6.egg
>>> creating
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Testing/ 
>>> Installation/PythonVirtualenv/lib/python2.6/site-packages/ 
>>> SimpleITK-0.3.0-py2.6.egg
>>> Extracting SimpleITK-0.3.0-py2.6.egg to
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Testing/ 
>>> Installation/PythonVirtualenv/lib/python2.6/site-packages
>>> Adding SimpleITK 0.3.0 to easy-install.pth file
>>>
>>> Installed
>>> /home/ajg23/GITROOT/SimpleITK/build/SimpleITK-build/Testing/ 
>>> Installation/PythonVirtualenv/lib/python2.6/site-packages/ 
>>> SimpleITK-0.3.0-py2.6.egg
>>> Processing dependencies for SimpleITK==0.3.0
>>> Finished processing dependencies for SimpleITK==0.3.0
>>> [ 57%] Built target _SimpleITK
>>> make[3]: *** [all] Error 2
>>> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK- 
>>> build] Error 2
>>> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>>
>>> ========================================================
>>>
>>> Bradley Lowekamp
>>>
>>> Medical Science and Computing for
>>>
>>> Office of High Performance Computing and Communications
>>>
>>> National Library of Medicine
>>>
>>> blowekamp at mail.nih.gov
>>>
>>>
>>>
>>>
>>>
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>>