Closed damientully closed 5 years ago
Hi,
I appear to be having the following error when trying to install flappie. Any assistance would be great.
Many thanks. Damien
dct7@login04:~/flappie$ openblasRoot=/home/dct7/bin/ make flappie cd build && \ cmake .. -DCMAKE_BUILD_TYPE=Release \ -DHDF5_ROOT='' \ -DOPENBLAS_REDHAT='' \ -DOPENBLAS_ROOT=/home/dct7/bin/ && \ make flappie -- Configuring done -- Generating done -- Build files have been written to: /home/dct7/flappie/build make[1]: Entering directory `/home/dct7/flappie/build' make[2]: Entering directory `/home/dct7/flappie/build' make[3]: Entering directory `/home/dct7/flappie/build' make[4]: Entering directory `/home/dct7/flappie/build' Scanning dependencies of target flappie_objects make[4]: Leaving directory `/home/dct7/flappie/build' make[4]: Entering directory `/home/dct7/flappie/build' [ 7%] Building C object CMakeFiles/flappie_objects.dir/src/decode.c.o /home/dct7/flappie/src/decode.c: In function ‘rle_trans_lookup’: /home/dct7/flappie/src/decode.c:896:46: warning: unused parameter ‘stay_to’ [-Wunused-parameter] size_t base_to, bool stay_to, ^~~~~~~ [ 15%] Building C object CMakeFiles/flappie_objects.dir/src/layers.c.o /home/dct7/flappie/src/layers.c: In function ‘rle_trans_lookup’: /home/dct7/flappie/src/layers.c:1238:60: warning: unused parameter ‘stay_to’ [-Wunused-parameter] size_t base_to, bool stay_to, ^~~~~~~ [ 23%] Building C object CMakeFiles/flappie_objects.dir/src/networks.c.o [ 30%] Building C object CMakeFiles/flappie_objects.dir/src/nnfeatures.c.o [ 38%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_common.c.o [ 46%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_matrix.c.o /home/dct7/flappie/src/flappie_matrix.c: In function ‘validate_flappie_matrix’: /home/dct7/flappie/src/flappie_matrix.c:150:45: warning: unused parameter ‘mat’ [-Wunused-parameter] bool validate_flappie_matrix(flappie_matrix mat, float lower, ^~~ /home/dct7/flappie/src/flappie_matrix.c:150:56: warning: unused parameter ‘lower’ [-Wunused-parameter] bool validate_flappie_matrix(flappie_matrix mat, float lower, ^~~~~ /home/dct7/flappie/src/flappie_matrix.c:151:43: warning: unused parameter ‘upper’ [-Wunused-parameter] const float upper, const float maskval, ^~~~~ /home/dct7/flappie/src/flappie_matrix.c:151:62: warning: unused parameter ‘maskval’ [-Wunused-parameter] const float upper, const float maskval, ^~~~~~~ /home/dct7/flappie/src/flappie_matrix.c:152:42: warning: unused parameter ‘only_finite’ [-Wunused-parameter] const bool only_finite, const char *file, ^~~~~~~~~~~ /home/dct7/flappie/src/flappie_matrix.c:152:67: warning: unused parameter ‘file’ [-Wunused-parameter] const bool only_finite, const char *file, ^~~~ /home/dct7/flappie/src/flappie_matrix.c:153:41: warning: unused parameter ‘line’ [-Wunused-parameter] const int line) { ^~~~ /home/dct7/flappie/src/flappie_matrix.c: In function ‘validate_vector’: /home/dct7/flappie/src/flappie_matrix.c:548:29: warning: unused parameter ‘vec’ [-Wunused-parameter] bool validate_vector(float *vec, const size_t n, const float lower, ^~~ /home/dct7/flappie/src/flappie_matrix.c:548:47: warning: unused parameter ‘n’ [-Wunused-parameter] bool validate_vector(float *vec, const size_t n, const float lower, ^ /home/dct7/flappie/src/flappie_matrix.c:548:62: warning: unused parameter ‘lower’ [-Wunused-parameter] bool validate_vector(float *vec, const size_t n, const float lower, ^~~~~ /home/dct7/flappie/src/flappie_matrix.c:549:34: warning: unused parameter ‘upper’ [-Wunused-parameter] const float upper, const char *file, const int line) { ^~~~~ /home/dct7/flappie/src/flappie_matrix.c:549:53: warning: unused parameter ‘file’ [-Wunused-parameter] const float upper, const char *file, const int line) { ^~~~ /home/dct7/flappie/src/flappie_matrix.c:549:69: warning: unused parameter ‘line’ [-Wunused-parameter] const float upper, const char *file, const int line) { ^~~~ /home/dct7/flappie/src/flappie_matrix.c: In function ‘validate_ivector’: /home/dct7/flappie/src/flappie_matrix.c:582:28: warning: unused parameter ‘vec’ [-Wunused-parameter] bool validate_ivector(int *vec, const size_t n, const int lower, const int upper, ^~~ /home/dct7/flappie/src/flappie_matrix.c:582:46: warning: unused parameter ‘n’ [-Wunused-parameter] bool validate_ivector(int *vec, const size_t n, const int lower, const int upper, ^ /home/dct7/flappie/src/flappie_matrix.c:582:59: warning: unused parameter ‘lower’ [-Wunused-parameter] bool validate_ivector(int *vec, const size_t n, const int lower, const int upper, ^~~~~ /home/dct7/flappie/src/flappie_matrix.c:582:76: warning: unused parameter ‘upper’ [-Wunused-parameter] bool validate_ivector(int *vec, const size_t n, const int lower, const int upper, ^~~~~ /home/dct7/flappie/src/flappie_matrix.c:583:35: warning: unused parameter ‘file’ [-Wunused-parameter] const char *file, const int line) { ^~~~ /home/dct7/flappie/src/flappie_matrix.c:583:51: warning: unused parameter ‘line’ [-Wunused-parameter] const char *file, const int line) { ^~~~ [ 53%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_output.c.o [ 61%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_structures.c.o [ 69%] Building C object CMakeFiles/flappie_objects.dir/src/util.c.o make[4]: Leaving directory `/home/dct7/flappie/build' [ 69%] Built target flappie_objects make[4]: Entering directory `/home/dct7/flappie/build' make[4]: Leaving directory `/home/dct7/flappie/build' make[4]: Entering directory `/home/dct7/flappie/build' [ 76%] Linking C static library libflappie.a make[4]: Leaving directory `/home/dct7/flappie/build' [ 76%] Built target flappie_static make[4]: Entering directory `/home/dct7/flappie/build' Scanning dependencies of target flappie make[4]: Leaving directory `/home/dct7/flappie/build' make[4]: Entering directory `/home/dct7/flappie/build' [ 84%] Building C object CMakeFiles/flappie.dir/src/fast5_interface.c.o /home/dct7/flappie/src/fast5_interface.c: In function ‘write_summary’: /home/dct7/flappie/src/fast5_interface.c:341:16: warning: unused variable ‘status2’ [-Wunused-variable] herr_t status2 = write_trace(read_group, trace_flat, res.trace->nr, res.trace->nc, ^~~~~~~ /home/dct7/flappie/src/fast5_interface.c:336:12: warning: unused variable ‘status’ [-Wunused-variable] herr_t status = write_signal(read_group, res.rt.raw + res.rt.start, ^~~~~~ [ 92%] Building C object CMakeFiles/flappie.dir/src/flappie.c.o [100%] Linking C executable flappie CMakeFiles/flappie.dir/src/flappie.c.o: In function `main': flappie.c:(.text.startup+0x7b6): undefined reference to `H5Fclose' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_float_attribute': fast5_interface.c:(.text+0x29): undefined reference to `H5Aopen' fast5_interface.c:(.text+0x36): undefined reference to `H5open' fast5_interface.c:(.text+0x3d): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0x4a): undefined reference to `H5Aread' fast5_interface.c:(.text+0x52): undefined reference to `H5Aclose' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `open_or_create_hdf5': fast5_interface.c:(.text+0x113): undefined reference to `H5check_version' fast5_interface.c:(.text+0x118): undefined reference to `H5open' fast5_interface.c:(.text+0x158): undefined reference to `H5check_version' fast5_interface.c:(.text+0x15d): undefined reference to `H5open' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `set_compression': fast5_interface.c:(.text+0x249): undefined reference to `H5open' fast5_interface.c:(.text+0x250): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g' fast5_interface.c:(.text+0x255): undefined reference to `H5Pcreate' fast5_interface.c:(.text+0x265): undefined reference to `H5Pset_shuffle' fast5_interface.c:(.text+0x26f): undefined reference to `H5Pset_deflate' fast5_interface.c:(.text+0x27d): undefined reference to `H5Pset_chunk' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_signal': fast5_interface.c:(.text+0x317): undefined reference to `H5Screate_simple' fast5_interface.c:(.text+0x324): undefined reference to `H5open' fast5_interface.c:(.text+0x32b): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g' fast5_interface.c:(.text+0x330): undefined reference to `H5Pcreate' fast5_interface.c:(.text+0x344): undefined reference to `H5Pset_shuffle' fast5_interface.c:(.text+0x34f): undefined reference to `H5Pset_deflate' fast5_interface.c:(.text+0x361): undefined reference to `H5Pset_chunk' fast5_interface.c:(.text+0x366): undefined reference to `H5open' fast5_interface.c:(.text+0x377): undefined reference to `H5T_IEEE_F32LE_g' fast5_interface.c:(.text+0x389): undefined reference to `H5Dcreate2' fast5_interface.c:(.text+0x391): undefined reference to `H5open' fast5_interface.c:(.text+0x3a0): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0x3aa): undefined reference to `H5Dwrite' fast5_interface.c:(.text+0x3b5): undefined reference to `H5Dclose' fast5_interface.c:(.text+0x3bd): undefined reference to `H5Pclose' fast5_interface.c:(.text+0x3c5): undefined reference to `H5Sclose' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_trace': fast5_interface.c:(.text+0x47e): undefined reference to `H5Screate_simple' fast5_interface.c:(.text+0x48b): undefined reference to `H5open' fast5_interface.c:(.text+0x492): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g' fast5_interface.c:(.text+0x497): undefined reference to `H5Pcreate' fast5_interface.c:(.text+0x4ab): undefined reference to `H5Pset_shuffle' fast5_interface.c:(.text+0x4b6): undefined reference to `H5Pset_deflate' fast5_interface.c:(.text+0x4c8): undefined reference to `H5Pset_chunk' fast5_interface.c:(.text+0x4cd): undefined reference to `H5open' fast5_interface.c:(.text+0x4de): undefined reference to `H5T_STD_U8LE_g' fast5_interface.c:(.text+0x4f0): undefined reference to `H5Dcreate2' fast5_interface.c:(.text+0x4f8): undefined reference to `H5open' fast5_interface.c:(.text+0x507): undefined reference to `H5T_NATIVE_INT_g' fast5_interface.c:(.text+0x511): undefined reference to `H5Dwrite' fast5_interface.c:(.text+0x51c): undefined reference to `H5Dclose' fast5_interface.c:(.text+0x524): undefined reference to `H5Pclose' fast5_interface.c:(.text+0x52c): undefined reference to `H5Sclose' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_string_attribute': fast5_interface.c:(.text+0x5b4): undefined reference to `H5Aopen' fast5_interface.c:(.text+0x5c8): undefined reference to `H5Aget_type' fast5_interface.c:(.text+0x5d8): undefined reference to `H5Tget_class' fast5_interface.c:(.text+0x5f4): undefined reference to `H5Tclose' fast5_interface.c:(.text+0x5fc): undefined reference to `H5Aclose' fast5_interface.c:(.text+0x64c): undefined reference to `H5Tis_variable_str' fast5_interface.c:(.text+0x65c): undefined reference to `H5Aget_space' fast5_interface.c:(.text+0x677): undefined reference to `H5Sget_simple_extent_dims' fast5_interface.c:(.text+0x690): undefined reference to `H5open' fast5_interface.c:(.text+0x697): undefined reference to `H5T_C_S1_g' fast5_interface.c:(.text+0x69c): undefined reference to `H5Tcopy' fast5_interface.c:(.text+0x6ae): undefined reference to `H5Tset_size' fast5_interface.c:(.text+0x6be): undefined reference to `H5Aread' fast5_interface.c:(.text+0x6ce): undefined reference to `H5Tclose' fast5_interface.c:(.text+0x6d6): undefined reference to `H5Sclose' fast5_interface.c:(.text+0x6e4): undefined reference to `H5Tget_size' fast5_interface.c:(.text+0x705): undefined reference to `H5Aread' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `get_raw_scaling': fast5_interface.c:(.text+0x7d4): undefined reference to `H5Gopen2' fast5_interface.c:(.text+0x7f7): undefined reference to `H5Aopen' fast5_interface.c:(.text+0x808): undefined reference to `H5open' fast5_interface.c:(.text+0x80f): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0x81c): undefined reference to `H5Aread' fast5_interface.c:(.text+0x824): undefined reference to `H5Aclose' fast5_interface.c:(.text+0x846): undefined reference to `H5Aopen' fast5_interface.c:(.text+0x857): undefined reference to `H5open' fast5_interface.c:(.text+0x85e): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0x86b): undefined reference to `H5Aread' fast5_interface.c:(.text+0x873): undefined reference to `H5Aclose' fast5_interface.c:(.text+0x895): undefined reference to `H5Aopen' fast5_interface.c:(.text+0x8a6): undefined reference to `H5open' fast5_interface.c:(.text+0x8ad): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0x8ba): undefined reference to `H5Aread' fast5_interface.c:(.text+0x8c2): undefined reference to `H5Aclose' fast5_interface.c:(.text+0x8e4): undefined reference to `H5Aopen' fast5_interface.c:(.text+0x8f5): undefined reference to `H5open' fast5_interface.c:(.text+0x8fc): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0x909): undefined reference to `H5Aread' fast5_interface.c:(.text+0x911): undefined reference to `H5Aclose' fast5_interface.c:(.text+0x91d): undefined reference to `H5Gclose' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_raw': fast5_interface.c:(.text+0xa78): undefined reference to `H5check_version' fast5_interface.c:(.text+0xa7d): undefined reference to `H5open' fast5_interface.c:(.text+0xa89): undefined reference to `H5Fopen' fast5_interface.c:(.text+0xaa0): undefined reference to `H5Eset_auto2' fast5_interface.c:(.text+0xabb): undefined reference to `H5Lget_name_by_idx' fast5_interface.c:(.text+0xafc): undefined reference to `H5Lget_name_by_idx' fast5_interface.c:(.text+0xb33): undefined reference to `H5Gopen2' fast5_interface.c:(.text+0xb5f): undefined reference to `H5Gclose' fast5_interface.c:(.text+0xb9b): undefined reference to `H5Dopen2' fast5_interface.c:(.text+0xbb1): undefined reference to `H5Dget_space' fast5_interface.c:(.text+0xbce): undefined reference to `H5Sget_simple_extent_dims' fast5_interface.c:(.text+0xbe5): undefined reference to `H5open' fast5_interface.c:(.text+0xbf6): undefined reference to `H5T_NATIVE_FLOAT_g' fast5_interface.c:(.text+0xc00): undefined reference to `H5Dread' fast5_interface.c:(.text+0xc28): undefined reference to `H5Sclose' fast5_interface.c:(.text+0xc32): undefined reference to `H5Dclose' fast5_interface.c:(.text+0xc7c): undefined reference to `H5Fclose' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_summary': fast5_interface.c:(.text+0x109c): undefined reference to `H5Gcreate2' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `open_or_create_hdf5': fast5_interface.c:(.text+0x13e): undefined reference to `H5Fcreate' fast5_interface.c:(.text+0x181): undefined reference to `H5Fopen' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `create_group': fast5_interface.c:(.text+0x1f0): undefined reference to `H5Gcreate2' CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_summary': fast5_interface.c:(.text+0x111d): undefined reference to `H5Gclose' collect2: error: ld returned 1 exit status make[4]: *** [flappie] Error 1 make[4]: Leaving directory `/home/dct7/flappie/build' make[3]: *** [CMakeFiles/flappie.dir/all] Error 2 make[3]: Leaving directory `/home/dct7/flappie/build' make[2]: *** [CMakeFiles/flappie.dir/rule] Error 2 make[2]: Leaving directory `/home/dct7/flappie/build' make[1]: *** [flappie] Error 2 make[1]: Leaving directory `/home/dct7/flappie/build' make: *** [build/flappie] Error 2
Hello, this is a HDF5 associated error. Since compilation has got this far, it must have found the hdf5.h header file but flappie cannot find the HDF5 library (libhdf5.so) to link to.
hdf5.h
libhdf5.so
Thanks. Fixed now.
Hi,
I appear to be having the following error when trying to install flappie. Any assistance would be great.
Many thanks. Damien