Bug#851142: caffe-contrib: FTBFS in sid: libboost_python.so: undefined reference to several Py* symbols

[Andreas Beckmann]

Source: caffe-contrib
Version: 1.0.0~rc3+20161127-g24d2f67-4
Severity: serious
Justification: fails to build from source

Hi,

caffe-contrib suddenly started to FTBFS in sid:

[...]
[100%] Linking CXX executable ../../../test/test.testbin
cd "/build/caffe-contrib-1.0.0~rc3+20161127-g24d2f67/caffe_cuda_build/src/caffe/test" && /usr/bin/cmake -E cmake_link_script CMakeFiles/test.testbin.dir/link.txt --verbose=1
/usr/bin/clang++-3.8   -g -O2 -fdebug-prefix-map=/build/caffe-contrib-1.0.0~rc3+20161127-g24d2f67=. -fstack-protector-strong -Wformat -Werror=format-security -Wall  -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wno-
sign-compare -Wno-uninitialized -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/test.testbin.dir/test_accuracy_layer.cpp.o CMakeFiles/test.testbin.dir/test_argmax_layer.cpp.o CMakeFiles/test.testbi
n.dir/test_batch_norm_layer.cpp.o CMakeFiles/test.testbin.dir/test_batch_reindex_layer.cpp.o CMakeFiles/test.testbin.dir/test_benchmark.cpp.o CMakeFiles/test.testbin.dir/test_bias_layer.cpp.o CMakeFiles/test.testbi
n.dir/test_blob.cpp.o CMakeFiles/test.testbin.dir/test_caffe_main.cpp.o CMakeFiles/test.testbin.dir/test_common.cpp.o CMakeFiles/test.testbin.dir/test_concat_layer.cpp.o CMakeFiles/test.testbin.dir/test_contrastive
_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_convolution_layer.cpp.o CMakeFiles/test.testbin.dir/test_crop_layer.cpp.o CMakeFiles/test.testbin.dir/test_data_layer.cpp.o CMakeFiles/test.testbin.dir/test_data_t
ransformer.cpp.o CMakeFiles/test.testbin.dir/test_db.cpp.o CMakeFiles/test.testbin.dir/test_deconvolution_layer.cpp.o CMakeFiles/test.testbin.dir/test_dummy_data_layer.cpp.o CMakeFiles/test.testbin.dir/test_eltwise
_layer.cpp.o CMakeFiles/test.testbin.dir/test_embed_layer.cpp.o CMakeFiles/test.testbin.dir/test_euclidean_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_filler.cpp.o CMakeFiles/test.testbin.dir/test_filter_laye
r.cpp.o CMakeFiles/test.testbin.dir/test_flatten_layer.cpp.o CMakeFiles/test.testbin.dir/test_gradient_based_solver.cpp.o CMakeFiles/test.testbin.dir/test_hdf5_output_layer.cpp.o CMakeFiles/test.testbin.dir/test_hd
f5data_layer.cpp.o CMakeFiles/test.testbin.dir/test_hinge_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_im2col_layer.cpp.o CMakeFiles/test.testbin.dir/test_image_data_layer.cpp.o CMakeFiles/test.testbin.dir/tes
t_infogain_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_inner_product_layer.cpp.o CMakeFiles/test.testbin.dir/test_internal_thread.cpp.o CMakeFiles/test.testbin.dir/test_io.cpp.o CMakeFiles/test.testbin.dir/te
st_layer_factory.cpp.o CMakeFiles/test.testbin.dir/test_lrn_layer.cpp.o CMakeFiles/test.testbin.dir/test_lstm_layer.cpp.o CMakeFiles/test.testbin.dir/test_math_functions.cpp.o CMakeFiles/test.testbin.dir/test_maxpo
ol_dropout_layers.cpp.o CMakeFiles/test.testbin.dir/test_memory_data_layer.cpp.o CMakeFiles/test.testbin.dir/test_multinomial_logistic_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_mvn_layer.cpp.o CMakeFiles/te
st.testbin.dir/test_net.cpp.o CMakeFiles/test.testbin.dir/test_neuron_layer.cpp.o CMakeFiles/test.testbin.dir/test_platform.cpp.o CMakeFiles/test.testbin.dir/test_pooling_layer.cpp.o CMakeFiles/test.testbin.dir/tes
t_power_layer.cpp.o CMakeFiles/test.testbin.dir/test_protobuf.cpp.o CMakeFiles/test.testbin.dir/test_random_number_generator.cpp.o CMakeFiles/test.testbin.dir/test_reduction_layer.cpp.o CMakeFiles/test.testbin.dir/
test_reshape_layer.cpp.o CMakeFiles/test.testbin.dir/test_rnn_layer.cpp.o CMakeFiles/test.testbin.dir/test_scale_layer.cpp.o CMakeFiles/test.testbin.dir/test_sigmoid_cross_entropy_loss_layer.cpp.o CMakeFiles/test.t
estbin.dir/test_slice_layer.cpp.o CMakeFiles/test.testbin.dir/test_softmax_layer.cpp.o CMakeFiles/test.testbin.dir/test_softmax_with_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_solver.cpp.o CMakeFiles/test.te
stbin.dir/test_solver_factory.cpp.o CMakeFiles/test.testbin.dir/test_split_layer.cpp.o CMakeFiles/test.testbin.dir/test_spp_layer.cpp.o CMakeFiles/test.testbin.dir/test_stochastic_pooling.cpp.o CMakeFiles/test.test
bin.dir/test_syncedmem.cpp.o CMakeFiles/test.testbin.dir/test_tanh_layer.cpp.o CMakeFiles/test.testbin.dir/test_threshold_layer.cpp.o CMakeFiles/test.testbin.dir/test_tile_layer.cpp.o CMakeFiles/test.testbin.dir/te
st_upgrade_proto.cpp.o CMakeFiles/test.testbin.dir/test_util_blas.cpp.o CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_test_im2col_kernel.cu.o  -o ../../../test/test.testbin -rdynamic ../../../lib/libgtest.
a ../../../lib/libcaffe.so.1.0.0-rc3 ../../../lib/libproto.a -lboost_system -lboost_thread -lboost_filesystem -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lpthread -lglog -lgflags -lprotobuf -lhdf5_cp
p /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lpthread -lglog -lgflags -lprotobuf -lhdf5_cpp /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lsz -lz -ldl -lm -lhdf5_hl_cpp /usr/lib/x86_64-linux-gn
u/hdf5/serial/libhdf5_hl.so -llmdb -lleveldb -lsnappy -lcudart -lcurand -lcublas -Wl,-Bstatic -lcublas_device -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libopencv_highgui.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_i
mgproc.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_core.so.2.4.9 -lblas -lpython3.5m -lboost_python
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyUnicodeUCS4_FromEncodedObject'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyNumber_InPlaceDivide'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_Size'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_FromStringAndSize'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_InternFromString'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyInt_AsLong'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyUnicodeUCS4_AsWideChar'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_AsString'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_FromFormat'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyClass_Type'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_FromString'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyFile_AsFile'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `Py_InitModule4_64'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyInt_Type'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyInt_FromLong'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyFile_FromString'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyNumber_Divide'
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.3.0/../../../x86_64-linux-gnu/libboost_python.so: undefined reference to `PyString_Type'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
src/caffe/test/CMakeFiles/test.testbin.dir/build.make:1888: recipe for target 'test/test.testbin' failed
make[5]: *** [test/test.testbin] Error 1
make[5]: Leaving directory '/build/caffe-contrib-1.0.0~rc3+20161127-g24d2f67/caffe_cuda_build'
CMakeFiles/Makefile2:333: recipe for target 'src/caffe/test/CMakeFiles/test.testbin.dir/all' failed
make[4]: *** [src/caffe/test/CMakeFiles/test.testbin.dir/all] Error 2
make[4]: Leaving directory '/build/caffe-contrib-1.0.0~rc3+20161127-g24d2f67/caffe_cuda_build'
CMakeFiles/Makefile2:340: recipe for target 'src/caffe/test/CMakeFiles/test.testbin.dir/rule' failed
make[3]: *** [src/caffe/test/CMakeFiles/test.testbin.dir/rule] Error 2


Andreas