Compiler error on Ubuntu -

[conchoecia]

I'm getting weird compiler errors where functions are "declared but never defined"!

System info

lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 15.10
Release:    15.10
Codename:   wily

make
gcc -std=gnu11 -c -Wall -O0 -g SeqPrep.c -o SeqPrep.o
SeqPrep.c: In function ‘main’:
SeqPrep.c:107:8: warning: variable ‘print_overhang’ set but not used [-Wunused-but-set-variable]
   bool print_overhang = false;
        ^
In file included from SeqPrep.c:10:0:
SeqPrep.c: At top level:
utils.h:80:20: warning: inline function ‘rev_qual’ declared but never defined
 extern inline void rev_qual( char q[], int len );
                    ^
utils.h:79:20: warning: inline function ‘revcom_char’ declared but never defined
 extern inline char revcom_char(const char base);
                    ^
utils.h:63:20: warning: inline function ‘f_r_id_check’ declared but never defined
 extern inline bool f_r_id_check( char fid[], size_t fid_len, char rid[], size_t rid_len );
                    ^
utils.h:62:19: warning: inline function ‘write_fastq’ declared but never defined
 extern inline int write_fastq(gzFile out, char id[], char seq[], char qual[]);
                   ^
utils.h:61:20: warning: inline function ‘next_fastqs’ declared but never defined
 extern inline bool next_fastqs( gzFile ffq, gzFile rfq, SQP curr_sqp, bool p64 );
                    ^
utils.h:49:20: warning: inline function ‘match_p33_merge’ declared but never defined
 extern inline char match_p33_merge(char pA, char pB);
                    ^
utils.h:48:20: warning: inline function ‘mismatch_p33_merge’ declared but never defined
 extern inline char mismatch_p33_merge(char pA, char pB);
                    ^
SeqPrep.c:81:23: warning: ‘spcount’ defined but not used [-Wunused-variable]
 static unsigned short spcount = 0;
                       ^
gcc -std=gnu11 -c -Wall -O0 -g utils.c -o utils.o
gcc -std=gnu11 -c -Wall -O0 -g stdaln.c -o stdaln.o
stdaln.c: In function ‘aln_local_core’:
stdaln.c:548:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
  int gap_open, gap_ext, b;
                         ^
stdaln.c: In function ‘aln_extend_core’:
stdaln.c:868:16: warning: variable ‘tmp_len’ set but not used [-Wunused-but-set-variable]
  int q, r, qr, tmp_len;
                ^
gcc -std=gnu11 SeqPrep.o utils.o stdaln.o -lz -lm -o SeqPrep
utils.o: In function `fill_merged_sequence':
/usr/local/bin/SeqPrep-1.1/utils.c:298: undefined reference to `gap_p33_qual'
/usr/local/bin/SeqPrep-1.1/utils.c:322: undefined reference to `gap_p33_qual'
collect2: error: ld returned 1 exit status
Makefile:13: recipe for target 'SeqPrep' failed
make: *** [SeqPrep] Error 1

I deleted your spinner progress bar function and the lines that called it, since it seemed like it was generating errors for other people.

Any ideas? I'm at UCSC too!

[conchoecia]

After giving up with editing the Makefile, the SeqPrep.c file, and the utils.h file, I pulled the latest version of the repo (commit 488ef06).

I didn't edit anything, ran make, and here is the resulting output.

make
cc  -c -Wall -O0 -g SeqPrep.c -o SeqPrep.o
SeqPrep.c: In function ‘main’:
SeqPrep.c:137:8: warning: variable ‘print_overhang’ set but not used [-Wunused-but-set-variable]
   bool print_overhang = false;
        ^
cc  -c -Wall -O0 -g utils.c -o utils.o
cc  -c -Wall -O0 -g stdaln.c -o stdaln.o
stdaln.c: In function ‘aln_local_core’:
stdaln.c:548:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
  int gap_open, gap_ext, b;
                         ^
stdaln.c: In function ‘aln_extend_core’:
stdaln.c:868:16: warning: variable ‘tmp_len’ set but not used [-Wunused-but-set-variable]
  int q, r, qr, tmp_len;
                ^
cc  SeqPrep.o utils.o stdaln.o -lz -lm -o SeqPrep

[jstjohn]

Cool! So it's working now?