[Debian-med-packaging] Fail to build SimpleITK with ITK v4.12

Ghislain Vaillant ghisvail at gmail.com
Sat Aug 12 09:51:23 UTC 2017


Dear all,

Since the update to ITK version 4.12 which recently landed in unstable, 
SimpleITK fails to build from source. The build log reports a failure to 
find the gdcm headers used by ITK. The error from the latest build on 
debomatic is pasted below:

```
cd /<<PKGBUILDDIR>>/SimpleITK-build/Code/IO/src && /usr/bin/c++ 
-DITK_IO_FACTORY_REGISTER_MANAGER -DSimpleITKIO_EXPORTS 
-I/<<PKGBUILDDIR>>/SimpleITK-build/Code/IO/src/ITKIOFactoryRegistration 
-I/usr/include/nifti -I/usr/include/gdcm-2.6 -isystem 
/usr/include/ITK-4.12 -I/<<PKGBUILDDIR>>/Code/IO/include 
-I/<<PKGBUILDDIR>>/Code/IO/src -I/<<PKGBUILDDIR>>/Code/Common/include 
-I/<<PKGBUILDDIR>>/SimpleITK-build/Code/Common/include  -g -O2 
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fPIC 
-fvisibility=hidden -fvisibility-inlines-hidden   -Wall -Wno-long-long 
-Wno-unused-local-typedefs -Wno-strict-overflow -Wextra -Wformat=2 
-Wno-format-nonliteral -Wunused -Wpointer-arith -Winvalid-pch 
-Wcast-align -Wdisabled-optimization -Woverloaded-virtual -Wshadow 
-Wwrite-strings -Wstrict-null-sentinel -Wno-invalid-offsetof -o 
CMakeFiles/SimpleITKIO.dir/sitkImportImageFilter.cxx.o -c 
/<<PKGBUILDDIR>>/Code/IO/src/sitkImportImageFilter.cxx
> cd /<<PKGBUILDDIR>>/SimpleITK-build/Code/IO/src && /usr/bin/c++  -DITK_IO_FACTORY_REGISTER_MANAGER -DSimpleITKIO_EXPORTS -I/<<PKGBUILDDIR>>/SimpleITK-build/Code/IO/src/ITKIOFactoryRegistration -I/usr/include/nifti -I/usr/include/gdcm-2.6 -isystem /usr/include/ITK-4.12 -I/<<PKGBUILDDIR>>/Code/IO/include -I/<<PKGBUILDDIR>>/Code/IO/src -I/<<PKGBUILDDIR>>/Code/Common/include -I/<<PKGBUILDDIR>>/SimpleITK-build/Code/Common/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fPIC -fvisibility=hidden -fvisibility-inlines-hidden   -Wall -Wno-long-long -Wno-unused-local-typedefs -Wno-strict-overflow -Wextra -Wformat=2 -Wno-format-nonliteral -Wunused -Wpointer-arith -Winvalid-pch -Wcast-align -Wdisabled-optimization -Woverloaded-virtual -Wshadow -Wwrite-strings -Wstrict-null-sentinel -Wno-invalid-offsetof -o CMakeFiles/SimpleITKIO.dir/sitkShow.cxx.o -c /<<PKGBUILDDIR>>/Code/IO/src/sitkShow.cxx
In file included from 
/<<PKGBUILDDIR>>/Code/IO/src/sitkImageSeriesReader.cxx:27:0:
/usr/include/ITK-4.12/itkGDCMSeriesFileNames.h:25:10: fatal error: 
gdcmSerieHelper.h: No such file or directory
  #include "gdcmSerieHelper.h"
           ^~~~~~~~~~~~~~~~~~~
compilation terminated.
Code/IO/src/CMakeFiles/SimpleITKIO.dir/build.make:137: recipe for target 
'Code/IO/src/CMakeFiles/SimpleITKIO.dir/sitkImageSeriesReader.cxx.o' failed
```

I am also concerned by the following detail: gdcm was recently bumped to 
the 2.8.x series, but the include directory is still 
`/usr/include/gdcm-2.6` according to the above build log. That sounds 
wrong to me.

Anyway, I confirm that builds of SimpleITK used to complete in the past 
(I used them to progressively refine the package-ability of SimpleITK 
together with upstream), so I suspect the build issue comes from the 
current ITK / GDCM stack available in unstable.

Could you guys please have a look?

Cheers,
Ghis


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