make  all-recursive
make[1]: Entering directory 'PBSIM-PacBio-Simulator'
Making all in src
make[2]: Entering directory 'PBSIM-PacBio-Simulator/src'
g++ -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT pbsim.o -MD -MP -MF .deps/pbsim.Tpo -c -o pbsim.o pbsim.cpp
pbsim.cpp: In function ‘int set_mut(sim_t*)’:
pbsim.cpp:1441:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   mut.sub_nt_a = "TGC";
                  ^~~~~
pbsim.cpp:1442:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   mut.sub_nt_t = "AGC";
                  ^~~~~
pbsim.cpp:1443:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   mut.sub_nt_g = "ATC";
                  ^~~~~
pbsim.cpp:1444:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   mut.sub_nt_c = "ATG";
                  ^~~~~
pbsim.cpp:1445:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   mut.sub_nt_n = "ATGC";
                  ^~~~~~
pbsim.cpp:1446:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   mut.ins_nt = "ATGC";
                ^~~~~~
mv -f .deps/pbsim.Tpo .deps/pbsim.Po
g++  -g -O2   -o pbsim pbsim.o
pbsim.o: In function `get_ref_inf(sim_t const*, ref_t*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:453: undefined reference to `trim(char*)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:492: undefined reference to `trim(char*)'
pbsim.o: In function `get_ref_seq(sim_t const*, ref_t*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:549: undefined reference to `trim(char*)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:558: undefined reference to `trim(char*)'
pbsim.o: In function `get_fastq_inf(sim_t const*, qc_t const*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:644: undefined reference to `trim(char*)'
pbsim.o:PBSIM-PacBio-Simulator/src/pbsim.cpp:610: more undefined references to `trim(char*)' follow
pbsim.o: In function `mutate(sim_t*, ref_t*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:1622: undefined reference to `revcomp(char*)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:1623: undefined reference to `revcomp(char*)'
pbsim.o: In function `simulate_by_sampling(sim_t*, ref_t*, mut_t*, fastq_t*, qc_t*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:1015: undefined reference to `trim(char*)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:1064: undefined reference to `count_digit(long)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:1067: undefined reference to `count_digit(long)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:1071: undefined reference to `count_digit(long)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:1072: undefined reference to `count_digit(long)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:1075: undefined reference to `count_digit(long)'
pbsim.o:/home/pierre/dev/PBSIM-PacBio-Simulator/src/pbsim.cpp:1076: more undefined references to `count_digit(long)' follow
pbsim.o: In function `set_model_qc(sim_t const*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:1653: undefined reference to `trim(char*)'
pbsim.o: In function `initialize_sim_process(sim_t*, fastq_t*, qc_t*)':
PBSIM-PacBio-Simulator/src/pbsim.cpp:166: undefined reference to `print_sim_param(sim_t const*)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:207: undefined reference to `print_fastq_stats(sim_t const*, fastq_t const*)'
pbsim.o: In function `main':
PBSIM-PacBio-Simulator/src/pbsim.cpp:62: undefined reference to `get_time_cpu()'
PBSIM-PacBio-Simulator/src/pbsim.cpp:63: undefined reference to `get_time()'
PBSIM-PacBio-Simulator/src/pbsim.cpp:135: undefined reference to `print_simulation_stats(sim_t const*, ref_t const*)'
PBSIM-PacBio-Simulator/src/pbsim.cpp:146: undefined reference to `get_time_cpu()'
PBSIM-PacBio-Simulator/src/pbsim.cpp:147: undefined reference to `get_time()'
PBSIM-PacBio-Simulator/src/pbsim.cpp:70: undefined reference to `print_help()'
collect2: error: ld returned 1 exit status
Makefile:208: recipe for target 'pbsim' failed
make[2]: *** [pbsim] Error 1
make[2]: Leaving directory '/home/pierre/dev/PBSIM-PacBio-Simulator/src'
Makefile:222: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/pierre/dev/PBSIM-PacBio-Simulator'
Makefile:161: recipe for target 'all' failed
make: *** [all] Error 2