Linking C executable flappie errors

[damientully]

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

[tmassingham-ont]

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.

[damientully]

Thanks. Fixed now.