[Debian-med-packaging] Bug#759971: plastimatch: FTBFS: make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so', needed by 'bragg_curve'. Stop.

[Lucas Nussbaum]

Source: plastimatch
Version: 1.5.16+dfsg-1
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20140830 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[3]: Entering directory '/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu'
> /usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/CMakeFiles 8
> make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so', needed by 'dlib_train'.  Stop.
> [ 83%] Building CXX object src/plastimatch/cli/CMakeFiles/landmark_warp.dir/landmark_warp_main.cxx.o
> make[3]: *** Waiting for unfinished jobs....
> cd /«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch/cli && /usr/bin/c++   -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -O3 -DNDEBUG -fPIC -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cli -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/util -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/sys -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/segment -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/qt -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/opencl -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/dose -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/clp -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/base -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/ITKIOFactoryRegistration -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/itk-3.20.0 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/DiffeomorphicDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/FastSymmetricForces -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/LOGDomainDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/nSIFT -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/bstrlib-05122010 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/dlib-17.46 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/liblbfgs-1.9/include -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac/Common -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/lua-5.1.4/src    -o CMakeFiles/landmark_warp.dir/landmark_warp_main.cxx.o -c /«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cli/landmark_warp_main.cxx
> [ 84%] Building CXX object src/plastimatch/standalone/CMakeFiles/compute_distance.dir/compute_distance.cxx.o
> cd /«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch/standalone && /usr/bin/c++   -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -O3 -DNDEBUG -fPIC -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone/standalone -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/util -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/sys -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/segment -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/qt -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/opencl -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/dose -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/clp -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cli -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/base -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/ITKIOFactoryRegistration -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/itk-3.20.0 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/DiffeomorphicDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/FastSymmetricForces -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/LOGDomainDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/nSIFT -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/bstrlib-05122010 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/dlib-17.46 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/liblbfgs-1.9/include -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac/Common    -o CMakeFiles/compute_distance.dir/compute_distance.cxx.o -c /«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone/compute_distance.cxx
> Building CXX object src/plastimatch/standalone/CMakeFiles/dlib_train.dir/dlib_train.cxx.o
> cd /«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch/standalone && /usr/bin/c++   -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -O3 -DNDEBUG -fPIC -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone/standalone -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/util -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/sys -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/segment -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/qt -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/opencl -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/dose -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/clp -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cli -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/base -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/ITKIOFactoryRegistration -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/itk-3.20.0 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/DiffeomorphicDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/FastSymmetricForces -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/LOGDomainDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/nSIFT -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/bstrlib-05122010 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/dlib-17.46 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/liblbfgs-1.9/include -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac/Common    -o CMakeFiles/dlib_train.dir/dlib_train.cxx.o -c /«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone/dlib_train.cxx
> /usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/CMakeFiles 
> make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so', needed by 'bragg_curve'.  Stop.
> make[3]: *** Waiting for unfinished jobs....
> [ 84%] Building CXX object src/plastimatch/standalone/CMakeFiles/bragg_curve.dir/bragg_curve_opts.cxx.o
> cd /«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch/standalone && /usr/bin/c++   -DITK_IO_FACTORY_REGISTER_MANAGER -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -O3 -DNDEBUG -fPIC -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone/standalone -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/util -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/sys -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/segment -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/register -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/reconstruct -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/qt -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/opencl -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cuda -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/dose -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/clp -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/cli -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/base -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu/ITKIOFactoryRegistration -I/home/steve/Packages/debian-med/trunk/packages/insighttoolkit/build-area/insighttoolkit4-4.6.0/BUILD/Modules/ThirdParty/HDF5/src -I/usr/include/dcmtk -I/usr/include/dcmtk/oflog -I/usr/include/dcmtk/ofstd -I/usr/include/dcmtk/dcmtls -I/usr/include/dcmtk/dcmsr -I/usr/include/dcmtk/dcmsign -I/usr/include/dcmtk/dcmqrdb -I/usr/include/dcmtk/dcmpstat -I/usr/include/dcmtk/dcmnet -I/usr/include/dcmtk/dcmjpls -I/usr/include/dcmtk/dcmjpeg -I/usr/include/dcmtk/dcmimgle -I/usr/include/dcmtk/dcmimage -I/usr/include/dcmtk/dcmdata -I/usr/include/dcmtk/config -I/usr/include/x86_64-linux-gnu -I/usr/include/gdcm-2.4 -I/usr/include/ITK-4.6 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/itk-3.20.0 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/DiffeomorphicDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/FastSymmetricForces -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/demons_itk_insight/LOGDomainDemons -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/nSIFT -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/bstrlib-05122010 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/dlib-17.46 -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/liblbfgs-1.9/include -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac -I/«BUILDDIR»/plastimatch-1.5.16+dfsg/libs/ransac/Common    -o CMakeFiles/bragg_curve.dir/bragg_curve_opts.cxx.o -c /«BUILDDIR»/plastimatch-1.5.16+dfsg/src/plastimatch/standalone/bragg_curve_opts.cxx
> make[3]: Leaving directory '/«BUILDDIR»/plastimatch-1.5.16+dfsg/obj-x86_64-linux-gnu'
> make[2]: *** [src/plastimatch/standalone/CMakeFiles/bragg_curve.dir/all] Error 2

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2014/08/30/plastimatch_1.5.16+dfsg-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures. The build
was done with DEB_BUILD_OPTIONS="parallel=4", so if your packaging tries
to support this, it might be a good idea to explore whether this might
be the cause of the failure.