[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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