compile error on Ubuntu

[jairideout]

After the latest pull request (#21) was merged to fix compile issues on OS X, I am unable to compile on Ubuntu:

$ make
cc  -c -Wall -O0 -g SeqPrep.c -o SeqPrep.o
SeqPrep.c: In function ‘main’:
SeqPrep.c:136:8: warning: variable ‘print_overhang’ set but not used [-Wunused-but-set-variable]
SeqPrep.c: At top level:
SeqPrep.c:108:5: warning: ‘spcount’ is static but used in inline function ‘update_spinner’ which is not static [enabled by default]
SeqPrep.c:90:12: warning: ‘spcount’ is static but used in inline function ‘update_spinner’ which is not static [enabled by default]
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]
stdaln.c: In function ‘aln_extend_core’:
stdaln.c:868:16: warning: variable ‘tmp_len’ set but not used [-Wunused-but-set-variable]
cc  SeqPrep.o utils.o stdaln.o -lz -lm -o SeqPrep
SeqPrep.o: In function `main':
/home/ubuntu/SeqPrep/SeqPrep.c:350: undefined reference to `update_spinner'
collect2: ld returned 1 exit status
make: *** [SeqPrep] Error 1

It seems that the issue is the extern keyword added to update_spinner (this line). When I remove extern, I'm able to successfully compile. I'm not sure how this will affect compatibility with OS X or other systems though.

System info:

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.2 LTS
Release:    12.04
Codename:   precise
$ uname -a
Linux ip-10-88-103-45 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
$ cc --version
cc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Please let me know if you need more info or if I can help in any way with testing/fixing this. Thanks!

[Cistron]

I have a very similar issue on our HPC cluster.

$make
gcc  -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;
        ^
SeqPrep.c: At top level:
SeqPrep.c:109:5: warning: ‘spcount’ is static but used in inline function ‘update_spinner’ which is not static
     spcount++;
     ^
SeqPrep.c:91:12: warning: ‘spcount’ is static but used in inline function ‘update_spinner’ which is not static
     switch(spcount % 4){
            ^
gcc  -c -Wall -O0 -g utils.c -o utils.o
gcc  -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  SeqPrep.o utils.o stdaln.o -lz -lm -o SeqPrep
SeqPrep.o: In function `main':
/home/sejj036/SeqPrep/SeqPrep.c:355: undefined reference to `update_spinner'
collect2: error: ld returned 1 exit status
make: *** [SeqPrep] Error 1

lsb_release -a
LSB Version:    :core-4.1-amd64:core-4.1-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 7.1 (Maipo)
Release:    7.1
Codename:   Maipo

$uname -a
Linux login06 3.10.0-123.20.1.el7.x86_64 #1 SMP Wed Jan 21 09:45:55 EST 2015 x86_64 x86_64 x86_64 GNU/Linux

$cc --version
cc (GCC) 4.8.3 20140911 (Red Hat 4.8.3-9)
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.```

[samdemorest]

@Cistron #33 should resolve this issue on your cluster. I discovered this solution while building this software for an HPC cluster I administer.