Cannot compile under OS X 10.10.2

[alexpreynolds]

I'm having some trouble compiling SeqPrep under Mac OS X 10.10.2:

balsamea:Github alexpreynolds$ git clone https://github.com/jstjohn/SeqPrep.git
balsamea:Github alexpreynolds$ cd SeqPrep/
balsamea:SeqPrep alexpreynolds$ make
gcc  -c -Wall -O0 -g SeqPrep.c -o SeqPrep.o
In file included from SeqPrep.c:10:
./utils.h:61:13: warning: inline function 'next_fastqs' is not defined [-Wundefined-inline]
inline bool next_fastqs( gzFile ffq, gzFile rfq, SQP curr_sqp, bool p64 );
            ^
SeqPrep.c:349:9: note: used here
  while(next_fastqs( ffq, rfq, sqp, p64 )){ //returns false when done
        ^
In file included from SeqPrep.c:10:
./utils.h:62:12: warning: inline function 'write_fastq' is not defined [-Wundefined-inline]
inline int write_fastq(gzFile out, char id[], char seq[], char qual[]);
           ^
SeqPrep.c:417:11: note: used here
          write_fastq(dffqw, sqp->fid, untrim_fseq, untrim_fqual);
          ^
In file included from SeqPrep.c:10:
./utils.h:80:13: warning: inline function 'rev_qual' is not defined [-Wundefined-inline]
inline void rev_qual( char q[], int len );
            ^
SeqPrep.c:428:9: note: used here
        rev_qual(sqp->rc_rqual, sqp->rlen);        //amd re-reverse the RC reads
        ^
3 warnings generated.
gcc  -c -Wall -O0 -g utils.c -o utils.o
utils.c:1062:3: warning: non-constant static local variable in inline function may be different in different files [-Wstatic-local-in-inline]
  static bool warned = false;
  ^
./utils.h:79:1: note: use 'static' to give inline function 'revcom_char' internal linkage
inline char revcom_char(const char base);
^
static 
1 warning generated.
gcc  -c -Wall -O0 -g stdaln.c -o stdaln.o
gcc  SeqPrep.o utils.o stdaln.o -lz -lm -o SeqPrep
Undefined symbols for architecture x86_64:
  "_gap_p33_qual", referenced from:
      _fill_merged_sequence in utils.o
  "_match_p33_merge", referenced from:
      _fill_merged_sequence in utils.o
      _read_merge in utils.o
      _adapter_merge in utils.o
  "_mismatch_p33_merge", referenced from:
      _fill_merged_sequence in utils.o
      _read_merge in utils.o
      _adapter_merge in utils.o
  "_next_fastqs", referenced from:
      _main in SeqPrep.o
  "_rev_qual", referenced from:
      _main in SeqPrep.o
      _make_blunt_ends in utils.o
      _adapter_trim in utils.o
      _read_olap_adapter_trim in utils.o
  "_revcom_char", referenced from:
      _revcom_seq in utils.o
  "_update_spinner", referenced from:
      _main in SeqPrep.o
  "_write_fastq", referenced from:
      _main in SeqPrep.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SeqPrep] Error 1

I am using clang/LLVM 3.5:

balsamea:SeqPrep alexpreynolds$ clang -v
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.1.0
Thread model: posix

I will shortly submit a pull request that shows patches that allowed compilation under this environment.

[alexpreynolds]

Cf. pull request #21