implicit declaration of function 'yyback' is invalid in C99 - xcode

Why is my lex build failing on Macos?
This is the error:
lex_yy.c:71:6: error: implicit declaration of function 'yywrap' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
if (yywrap()) return(0); break;
lex_yy.c:68:14: error: implicit declaration of function 'yylook' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
while( (nstr = yylook()) >= 0)
and
lex_yy.c:874:12: error: implicit declaration of function 'yyback' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
while(yyback((*lsp)->yystops,-*yyfnd) != 1 && lsp > yylstate){

Related

What does --with-cflags="-Wno-error=implicit-function-declaration" do?

I was struggling to install thin as a dependency in a Ruby project, when I came across this solution here: https://github.com/macournoyer/thin/issues/365#issuecomment-692063842 (gem install thin -v '1.7.2' -- --with-cflags="-Wno-error=implicit-function-declaration")
It works, but I'm not very familiar with Ruby so have no idea why. What is this flag doing? Why does it make the install work without any issues?
The error I was getting before this fix:
❯ gem install thin -v '1.7.2'
Building native extensions. This could take a while...
ERROR: Error installing thin:
ERROR: Failed to build gem native extension.
current directory: /Users/XXX/.gem/ruby/2.7.1/gems/thin-1.7.2/ext/thin_parser
/Users/XXX/.rubies/ruby-2.7.1/bin/ruby -I /Users/XXX/.rubies/ruby-2.7.1/lib/ruby/2.7.0 -r ./siteconf20210923-79304-z21dcg.rb extconf.rb
checking for main() in -lc... yes
creating Makefile
current directory: /Users/XXX/.gem/ruby/2.7.1/gems/thin-1.7.2/ext/thin_parser
make "DESTDIR=" clean
current directory: /Users/XXX/.gem/ruby/2.7.1/gems/thin-1.7.2/ext/thin_parser
make "DESTDIR="
compiling parser.c
parser.c:31:18: warning: unused variable 'http_parser_en_main' [-Wunused-const-variable]
static const int http_parser_en_main = 1;
^
1 warning generated.
compiling thin.c
thin.c:242:3: error: implicit declaration of function 'thin_http_parser_init' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
thin_http_parser_init(hp);
^
thin.c:242:3: note: did you mean 'http_parser_init'?
./parser.h:41:5: note: 'http_parser_init' declared here
int http_parser_init(http_parser *parser);
^
thin.c:260:3: error: implicit declaration of function 'thin_http_parser_init' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
thin_http_parser_init(http);
^
thin.c:277:3: error: implicit declaration of function 'thin_http_parser_init' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
thin_http_parser_init(http);
^
thin.c:294:3: error: implicit declaration of function 'thin_http_parser_finish' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
thin_http_parser_finish(http);
^
thin.c:294:3: note: did you mean 'Thin_HttpParser_finish'?
thin.c:290:7: note: 'Thin_HttpParser_finish' declared here
VALUE Thin_HttpParser_finish(VALUE self)
^
thin.c:296:10: error: implicit declaration of function 'thin_http_parser_is_finished' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
return thin_http_parser_is_finished(http) ? Qtrue : Qfalse;
^
thin.c:334:5: error: implicit declaration of function 'thin_http_parser_execute' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
thin_http_parser_execute(http, dptr, dlen, from);
^
thin.c:334:5: note: did you mean 'Thin_HttpParser_execute'?
thin.c:317:7: note: 'Thin_HttpParser_execute' declared here
VALUE Thin_HttpParser_execute(VALUE self, VALUE req_hash, VALUE data, VALUE start)
^
thin.c:338:8: error: implicit declaration of function 'thin_http_parser_has_error' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
if(thin_http_parser_has_error(http)) {
^
thin.c:338:8: note: did you mean 'http_parser_has_error'?
./parser.h:44:5: note: 'http_parser_has_error' declared here
int http_parser_has_error(http_parser *parser);
^
thin.c:359:10: error: implicit declaration of function 'thin_http_parser_has_error' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
return thin_http_parser_has_error(http) ? Qtrue : Qfalse;
^
thin.c:374:10: error: implicit declaration of function 'thin_http_parser_is_finished' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
return thin_http_parser_is_finished(http) ? Qtrue : Qfalse;
^
9 errors generated.
make: *** [thin.o] Error 1
make failed, exit code 2
Gem files will remain installed in /Users/XXX/.gem/ruby/2.7.1/gems/thin-1.7.2 for inspection.
Results logged to /Users/XXX/.gem/ruby/2.7.1/extensions/x86_64-darwin-19/2.7.0-static/thin-1.7.2/gem_make.out
I didn't read the stack trace properly...
It looks like this flag is basically telling the compiler to ignore where functions are implicitly declared rather than erroring out when this happens.

puma gem and ssl errors while doing bundle install

I am running bundle install to gems but it is failing for some gems.
Currently, it's breaking for puma gem (An error occurred while installing puma (3.6.0), and Bundler cannot continue).
these are the logs for the same
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/Users/pusingh/.rvm/gems/ruby-2.3.7#pm/extensions/x86_64-darwin-19/2.3.0/puma-3.6.0/mkmf.log
current directory: /Users/pusingh/.rvm/gems/ruby-2.3.7#pm/gems/puma-3.6.0/ext/puma_http11
make "DESTDIR=" clean
current directory: /Users/pusingh/.rvm/gems/ruby-2.3.7#pm/gems/puma-3.6.0/ext/puma_http11
make "DESTDIR="
compiling http11_parser.c
ext/puma_http11/http11_parser.rl:111:17: warning: comparison of integers of different signs: 'long' and 'unsigned long'
[-Wsign-compare]
assert(pe - p == len - off && "pointers aren't same distance");
~~~~~~ ^ ~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
(__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
^
ext/puma_http11/http11_parser.c:43:18: warning: unused variable 'puma_parser_en_main' [-Wunused-const-variable]
static const int puma_parser_en_main = 1;
^
2 warnings generated.
compiling io_buffer.c
compiling mini_ssl.c
mini_ssl.c:90:5: error: incomplete definition of type 'struct dh_st'
dh->p = BN_bin2bn(dh1024_p, sizeof(dh1024_p), NULL);
~~^
/usr/local/opt/openssl/include/openssl/ossl_typ.h:104:16: note: forward declaration of 'struct dh_st'
typedef struct dh_st DH;
^
mini_ssl.c:91:5: error: incomplete definition of type 'struct dh_st'
dh->g = BN_bin2bn(dh1024_g, sizeof(dh1024_g), NULL);
~~^
/usr/local/opt/openssl/include/openssl/ossl_typ.h:104:16: note: forward declaration of 'struct dh_st'
typedef struct dh_st DH;
^
mini_ssl.c:93:10: error: incomplete definition of type 'struct dh_st'
if ((dh->p == NULL) || (dh->g == NULL)) {
~~^
/usr/local/opt/openssl/include/openssl/ossl_typ.h:104:16: note: forward declaration of 'struct dh_st'
typedef struct dh_st DH;
^
mini_ssl.c:93:29: error: incomplete definition of type 'struct dh_st'
if ((dh->p == NULL) || (dh->g == NULL)) {
~~^
/usr/local/opt/openssl/include/openssl/ossl_typ.h:104:16: note: forward declaration of 'struct dh_st'
typedef struct dh_st DH;
^
mini_ssl.c:197:27: warning: 'DTLSv1_method' is deprecated [-Wdeprecated-declarations]
conn->ctx = SSL_CTX_new(DTLSv1_method());
^
/usr/local/opt/openssl/include/openssl/ssl.h:1895:1: note: 'DTLSv1_method' has been explicitly marked deprecated here
DEPRECATEDIN_1_1_0(__owur const SSL_METHOD *DTLSv1_method(void)) /* DTLSv1.0 */
^
/usr/local/opt/openssl/include/openssl/opensslconf.h:155:34: note: expanded from macro 'DEPRECATEDIN_1_1_0'
# define DEPRECATEDIN_1_1_0(f) DECLARE_DEPRECATED(f)
^
/usr/local/opt/openssl/include/openssl/opensslconf.h:118:55: note: expanded from macro 'DECLARE_DEPRECATED'
# define DECLARE_DEPRECATED(f) f __attribute__ ((deprecated));
^
mini_ssl.c:233:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int verify_err = SSL_get_verify_result(ssl);
~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~
mini_ssl.c:246:13: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
err = ERR_get_error();
~ ^~~~~~~~~~~~~~~
3 warnings and 4 errors generated.
make: *** [mini_ssl.o] Error 1
make failed, exit code 2
I am using ruby 2.3.7 with catalina mac os 10.15.5 Please help

Why does this template work in a single file but not across files?

Consider array.sats:
#include "share/atspre_staload.hats"
fun {a:t#ype} make: (int, a) -> void
array.dats:
#include "share/atspre_staload.hats"
staload "./array.sats"
implement {a} make(n: int, x: a) = ()
and example.dats:
staload Array = "./array.sats"
implement main0() = () where {
val arr = $Array.make<int>(10, 42)
}
These fail to compile with a bunch of template errors:
$ make clean all
rm -fv *_[sd]ats.[co] example
removed 'array_dats.c'
removed 'array_dats.o'
removed 'array_sats.c'
removed 'array_sats.o'
removed 'example_dats.c'
patscc -DATS_MEMALLOC_GCBDW -c array.sats
clang: warning: argument unused during compilation: '-L/usr/local/lib/ats2-postiats-0.3.9/ccomp/atslib/lib' [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: '-L/usr/local/lib/ats2-postiats-0.3.9/ccomp/atslib/lib64' [-Wunused-command-line-argument]
patscc -DATS_MEMALLOC_GCBDW -c array.dats
clang: warning: argument unused during compilation: '-L/usr/local/lib/ats2-postiats-0.3.9/ccomp/atslib/lib' [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: '-L/usr/local/lib/ats2-postiats-0.3.9/ccomp/atslib/lib64' [-Wunused-command-line-argument]
patscc -DATS_MEMALLOC_GCBDW -o example example.dats -lgc
example_dats.c:169:23: error: use of undeclared identifier 'PMVtmpltcstmat'
ATSINSmove_void(tmp1, PMVtmpltcstmat[0](make<S2Eapp(S2Ecst(g0int_t0ype); S2Eextkind(atstype_int))>)(ATSPMVi0nt(10), ATSPMVi0nt(42))) ;
^
example_dats.c:169:46: warning: implicit declaration of function 'S2Eapp' is invalid in C99 [-Wimplicit-function-declaration]
ATSINSmove_void(tmp1, PMVtmpltcstmat[0](make<S2Eapp(S2Ecst(g0int_t0ype); S2Eextkind(atstype_int))>)(ATSPMVi0nt(10), ATSPMVi0nt(42))) ;
^
example_dats.c:169:53: warning: implicit declaration of function 'S2Ecst' is invalid in C99 [-Wimplicit-function-declaration]
ATSINSmove_void(tmp1, PMVtmpltcstmat[0](make<S2Eapp(S2Ecst(g0int_t0ype); S2Eextkind(atstype_int))>)(ATSPMVi0nt(10), ATSPMVi0nt(42))) ;
^
example_dats.c:169:60: error: use of undeclared identifier 'g0int_t0ype'
ATSINSmove_void(tmp1, PMVtmpltcstmat[0](make<S2Eapp(S2Ecst(g0int_t0ype); S2Eextkind(atstype_int))>)(ATSPMVi0nt(10), ATSPMVi0nt(42))) ;
^
example_dats.c:169:41: error: use of undeclared identifier 'make'
ATSINSmove_void(tmp1, PMVtmpltcstmat[0](make<S2Eapp(S2Ecst(g0int_t0ype); S2Eextkind(atstype_int))>)(ATSPMVi0nt(10), ATSPMVi0nt(42))) ;
^
example_dats.c:169:99: error: expected expression
ATSINSmove_void(tmp1, PMVtmpltcstmat[0](make<S2Eapp(S2Ecst(g0int_t0ype); S2Eextkind(atstype_int))>)(ATSPMVi0nt(10), ATSPMVi0nt(42))) ;
^
2 warnings and 4 errors generated.
make: *** [example] Error 1
Meanwhile the same content in a single file compiles and runs without error:
#include "share/atspre_staload.hats"
extern fun {a:t#ype} make: (int, a) -> void
#include "share/atspre_staload.hats"
implement {a} make(n: int, x: a) = ()
implement main0() = () where {
val arr = make<int>(10, 42)
}
What's wrong with the separated code? Very similar code in the $UNSAFE files seems to work fine with templates and with a namespace.
You also need to staload array.dats:
staload Array = "./array.sats"
staload _(*Array*) = "./array.dats"
implement main0() = () where {
val arr = $Array.make<int>(10, 42)
}

EGlib 2.6.20 does not install (trying to install SCIP)

I am trying to solve an integer linear program using SCIP. The beta version that I require (for exact solving) is given at:
http://scip.zib.de/#exact
As linked there, the source code is at:
http://scip.zib.de/download.php?fname=scip-3.0.0-ex.tgz
I followed the INSTALL file. It requires the installation of EGlib 2.6.20. However, this installation fails during 'make' with the following error:
phani#OptiPlex-9030-AIO ~/EGlib-2.6.20 $ make
make[1]: Entering directory '/home/phani/EGlib-2.6.20'
make[1]: Leaving directory '/home/phani/EGlib-2.6.20'
make[1]: Entering directory '/home/phani/EGlib-2.6.20'
Building include/EGlib.h
Compiling src/eg_bit.c
Compiling src/eg_compare.c
Compiling src/eg_io.c
src/eg_io.c: In function ‘EGioGets’:
src/eg_io.c:618:7: warning: unused variable ‘b’ [-Wunused-variable]
char*b = buf;
^
src/eg_io.c: In function ‘EGioEof’:
src/eg_io.c:648:6: warning: unused variable ‘err’ [-Wunused-variable]
int err;
^
src/eg_io.c: In function ‘EGmvar’:
src/eg_io.c:42:2: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs]
va_start (largs, nind);
^
Compiling src/eg_lpnum.c
Compiling src/eg_net.c
Compiling src/eg_random.c
Compiling src/eg_macros.c
Compiling src/eg_ehash.c
Compiling src/eg_perm_it.c
Compiling src/eg_symtab.c
Compiling src/eg_keytab.c
Compiling src/eg_simula.c
In file included from src/eg_simula.c:25:0:
src/eg_simula.h:227:2: error: unknown type name ‘dbl_EGeHeapCn_t’
dbl_EGeHeapCn_t heap_cn;/**< connector in the heap containing the agent */
^
src/eg_simula.h:240:2: error: unknown type name ‘dbl_EGeHeap_t’
dbl_EGeHeap_t hp; /**< Heap containing events to be processed */
^
src/eg_simula.c: In function ‘EGsimExp’:
src/eg_simula.c:29:30: warning: unused parameter ‘t’ [-Wunused-parameter]
double EGsimExp(const double t, void*const data)
^
src/eg_simula.c: In function ‘EGsimUniform’:
src/eg_simula.c:40:34: warning: unused parameter ‘t’ [-Wunused-parameter]
double EGsimUniform(const double t, void*const data)
^
src/eg_simula.c: In function ‘EGsimNormal’:
src/eg_simula.c:51:33: warning: unused parameter ‘t’ [-Wunused-parameter]
double EGsimNormal(const double t, void*const data)
^
In file included from src/eg_simula.c:25:0:
src/eg_simula.c: In function ‘EGsimNewEvent’:
src/eg_simula.h:277:2: warning: implicit declaration of function ‘dbl_EGeHeapCnInit’ [-Wimplicit-function-declaration]
dbl_EGeHeapCnInit(&(__EGsimA->heap_cn));\
^
src/eg_simula.c:73:2: note: in expansion of macro ‘EGsimSetAgent’
EGsimSetAgent(la,sim->cur_time + gen->gen(sim->cur_time,gen->data));
^
src/eg_simula.c:74:13: error: request for member ‘val’ in something not a structure or union
la->heap_cn.val = la->last_time;
^
src/eg_simula.c:77:12: error: request for member ‘sz’ in something not a structure or union
if(sim->hp.sz == sim->hp.max_sz)
^
src/eg_simula.c:77:26: error: request for member ‘max_sz’ in something not a structure or union
if(sim->hp.sz == sim->hp.max_sz)
^
src/eg_simula.c:78:3: warning: implicit declaration of function ‘dbl_EGeHeapResize’ [-Wimplicit-function-declaration]
dbl_EGeHeapResize(&(sim->hp),sim->hp.sz*2);
^
src/eg_simula.c:78:39: error: request for member ‘sz’ in something not a structure or union
dbl_EGeHeapResize(&(sim->hp),sim->hp.sz*2);
^
src/eg_simula.c:80:9: warning: implicit declaration of function ‘dbl_EGeHeapAdd’ [-Wimplicit-function-declaration]
rval = dbl_EGeHeapAdd(&(sim->hp),&(la->heap_cn));
^
In file included from src/eg_simula.h:47:0,
from src/eg_simula.c:25:
src/eg_simula.c:85:55: error: request for member ‘val’ in something not a structure or union
MESSAGE(EG_SIM_VERBOSE,"new Agent at %lf",la->heap_cn.val);
^
src/eg_macros.h:246:18: note: in definition of macro ‘MESSAGE’
fprintf(stderr,__VA_ARGS__);\
^
In file included from src/eg_simula.h:47:0,
from src/eg_simula.c:25:
src/eg_simula.c: In function ‘EGsim’:
src/eg_simula.c:284:22: warning: implicit declaration of function ‘dbl_EGeHeapGetMin’ [-Wimplicit-function-declaration]
ca = EGcontainerOf(dbl_EGeHeapGetMin(&(sim->hp)), EGsimAgent_t,heap_cn);
^
src/eg_macros.h:134:56: note: in definition of macro ‘EGcontainerOf’
typeof(((__type *)0)->__member) *const __EGcOf_ptr = (__ptr);\
^
src/eg_macros.h:134:55: warning: initialization makes pointer from integer without a cast [-Wint-conversion]
typeof(((__type *)0)->__member) *const __EGcOf_ptr = (__ptr);\
^
src/eg_simula.c:284:8: note: in expansion of macro ‘EGcontainerOf’
ca = EGcontainerOf(dbl_EGeHeapGetMin(&(sim->hp)), EGsimAgent_t,heap_cn);
^
src/eg_simula.c:285:30: error: request for member ‘val’ in something not a structure or union
sim->cur_time = ca->heap_cn.val;
^
src/eg_simula.c:327:17: error: request for member ‘val’ in something not a structure or union
na->heap_cn.val = sim->cur_time + cn->gen(sim->cur_time,cn->data);
^
src/eg_simula.c:328:6: warning: implicit declaration of function ‘dbl_EGeHeapSiftUp’ [-Wimplicit-function-declaration]
dbl_EGeHeapSiftUp(&(sim->hp),&(na->heap_cn));
^
src/eg_simula.c:365:17: error: request for member ‘val’ in something not a structure or union
ca->heap_cn.val = sim->cur_time;
^
src/eg_simula.c:371:17: error: request for member ‘val’ in something not a structure or union
ca->heap_cn.val = sim->cur_time + nn->gen(sim->cur_time,nn->data);
^
src/eg_simula.c:377:17: error: request for member ‘val’ in something not a structure or union
ca->heap_cn.val = DBL_MAX;
^
src/eg_simula.c:381:12: warning: implicit declaration of function ‘dbl_EGeHeapSiftDown’ [-Wimplicit-function-declaration]
rval = dbl_EGeHeapSiftDown(&(sim->hp),&(ca->heap_cn));
^
src/eg_simula.c:388:5: warning: implicit declaration of function ‘dbl_EGeHeapDel’ [-Wimplicit-function-declaration]
dbl_EGeHeapDel(&(sim->hp),&(ca->heap_cn));
^
src/eg_simula.c:429:17: error: request for member ‘val’ in something not a structure or union
ca->heap_cn.val = sim->cur_time;
^
src/eg_simula.c:433:17: error: request for member ‘val’ in something not a structure or union
ca->heap_cn.val = sim->cur_time + nn->gen(sim->cur_time,nn->data);
^
src/eg_simula.c:441:17: error: request for member ‘val’ in something not a structure or union
ca->heap_cn.val = DBL_MAX;
^
Makefile.library:38: recipe for target 'obj/eg_simula.o' failed
make[1]: *** [obj/eg_simula.o] Error 1
make[1]: Leaving directory '/home/phani/EGlib-2.6.20'
Makefile:23: recipe for target 'library' failed
make: *** [library] Error 2
After some searching, I have noticed that dbl_EGeHeap_t is not defined in the source code, and that seems to be throwing errors.
On searching online, it seems to be the case that it was defined in EGlib 2.6.15 (https://conexo.dii.uchile.cl/SVN/EGlib/EGlib2/tags/EGlib-2.6.15/TEmplate/dbl_eg_eheap.h), but the corresponding file in 2.6.20 does not have the definition.
Has anybody else experienced this? I badly need a solution to this.

GCC/G++ Errors Mac OS X Yosemite

since some weeks, I'm working with a new Mac which works with OS X Yosemite (Version 10.10.3). I figured out a lot of trouble installing programs from source, why I already changed the compiler to, e.g., gcc 4.2, 4.7, and 4.9. Furthermore, I "removed" the connection to clang, but also this produces still errors during compiling. However, doing the same on a Mac OS X machine version 10.7.5 works fine. There, gcc version 4.2.1 is running.
Here's an example error message, I get typing make in the command line:
cc -O2 -c -o swat.o swat.c
In file included from swat.c:25:
./swat.h:85:35: warning: '/*' within block comment [-Wcomment]
/* int *maxstu_vec; NOT NEEDED /* array of length length + 1, used to hold row of scores,
^
swat.c:29:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
compare_scores(entry1, entry2)
^
swat.c:35:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
compare_z_scores(entry1, entry2)
^
swat.c:42:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
compare_E_values(entry1, entry2)
^
swat.c:49:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
main(argc,argv)
^
swat.c:75:3: warning: implicit declaration of function 'get_parameters' is invalid in C99 [-Wimplicit-function-declaration]
get_parameters(argc, argv, "swat");
^
swat.c:85:3: warning: implicit declaration of function 'alloc_hist' is invalid in C99 [-Wimplicit-function-declaration]
alloc_hist();
^
swat.c:86:10: warning: implicit declaration of function 'get_next_file_entry' is invalid in C99 [-Wimplicit-function-declaration]
while (get_next_file_entry(qdb)) {
^
swat.c:95:5: warning: implicit declaration of function 'notify' is invalid in C99 [-Wimplicit-function-declaration]
notify("Searching: ");
^
swat.c:98:12: warning: implicit declaration of function 'append_seq_entry' is invalid in C99 [-Wimplicit-function-declaration]
s_entry = append_seq_entry(sdb);
^
swat.c:110:2: warning: implicit declaration of function 'set_score' is invalid in C99 [-Wimplicit-function-declaration]
set_score(s_entry, score);
^
swat.c:127:57: warning: implicit declaration of function 'get_seq_length' is invalid in C99 [-Wimplicit-function-declaration]
score = parameters->align(q_profile, get_seq(s_entry), get_seq_length(s_entry), 1, 0, 0, 0, 0, 0);
^
swat.c:146:5: warning: implicit declaration of function 'initialize_hist' is invalid in C99 [-Wimplicit-function-declaration]
initialize_hist();
^
swat.c:155:7: warning: implicit declaration of function 'update_hist' is invalid in C99 [-Wimplicit-function-declaration]
update_hist(score_entry, 0);
^
swat.c:158:5: warning: implicit declaration of function 'process_hist' is invalid in C99 [-Wimplicit-function-declaration]
process_hist();
^
swat.c:172:2: warning: implicit declaration of function 'fit_log_n' is invalid in C99 [-Wimplicit-function-declaration]
fit_log_n(q_length);
^
swat.c:175:4: warning: implicit declaration of function 'find_z' is invalid in C99 [-Wimplicit-function-declaration]
find_z(score_entry);
^
swat.c:195:9: warning: implicit declaration of function 'reject_entry' is invalid in C99 [-Wimplicit-function-declaration]
if (!reject_entry(score_entry)) nz++; /* assumes Smith-Waterman */
^
swat.c:202:7: warning: implicit declaration of function 'new_est_lambda_K' is invalid in C99 [-Wimplicit-function-declaration]
new_est_lambda_K(q_length, score_entries, last_score_entry);
^
swat.c:242:24: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (parameters->use_n && score_entry >= score_entries + parameters->max_num_alignments
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
swat.c:242:24: note: place parentheses around the '&&' expression to silence this warning
if (parameters->use_n && score_entry >= score_entries + parameters->max_num_alignments
^
( )
swat.c:243:24: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| parameters->use_z && score_entry->z < parameters->z_cutoff || !score_entry->score)
~~ ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
swat.c:243:24: note: place parentheses around the '&&' expression to silence this warning
|| parameters->use_z && score_entry->z < parameters->z_cutoff || !score_entry->score)
^
( )
swat.c:256:29: warning: data argument not used by format string [-Wformat-extra-args]
score_entry->score, score_entry->z, e_value, score_entry->E);
^
swat.c:261:2: warning: implicit declaration of function 'print_alignment' is invalid in C99 [-Wimplicit-function-declaration]
print_alignment(q_profile);
^
swat.c:266:65: warning: data argument not used by format string [-Wformat-extra-args]
get_id(seq_num), get_seq_length(seq_num), score_entry->score, score_entry->z);
^
swat.c:272:5: warning: implicit declaration of function 'free_profile' is invalid in C99 [-Wimplicit-function-declaration]
free_profile(q_profile);
^
25 warnings generated.
cc -O2 -c -o weibull.o weibull.c
In file included from weibull.c:25:
./swat.h:85:35: warning: '/*' within block comment [-Wcomment]
/* int *maxstu_vec; NOT NEEDED /* array of length length + 1, used to hold row of scores,
^
weibull.c:47:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
reject_entry(score_entry)
^
weibull.c:50:32: warning: '&&' within '||' [-Wlogical-op-parentheses]
return (!parameters->nw_flag && !score_entry->score || score_entry->length < LENGTH_CUTOFF);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ ~~
weibull.c:50:32: note: place parentheses around the '&&' expression to silence this warning
return (!parameters->nw_flag && !score_entry->score || score_entry->length < LENGTH_CUTOFF);
^
( )
weibull.c:53:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
alloc_hist()
^
weibull.c:65:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
weibull.c:67:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
initialize_hist()
^
weibull.c:78:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
weibull.c:80:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
update_hist(score_entry, z_flag)
^
weibull.c:88:5: error: non-void function 'update_hist' should return a value [-Wreturn-type]
return;
^
weibull.c:92:5: error: non-void function 'update_hist' should return a value [-Wreturn-type]
return;
^
weibull.c:106:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
prune_hist(score_entry)
^
weibull.c:111:34: error: non-void function 'prune_hist' should return a value [-Wreturn-type]
if (reject_entry(score_entry)) return;
^
weibull.c:127:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
process_hist()
^
weibull.c:155:5: warning: implicit declaration of function 'fatalError' is invalid in C99 [-Wimplicit-function-declaration]
fatalError("No entries have scores exceeding -gap_init");
^
weibull.c:168:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
fit_log_n(q_length)
^
weibull.c:300:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
est_lambda_K(q_length)
^
weibull.c:399:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
new_est_lambda_K(q_length, score_entries, last_score_entry) /* using non-extreme-value dist'n */
^
weibull.c:644:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
find_z(entry)
^
weibull.c:652:21: warning: implicit declaration of function 'make_log_table' is invalid in C99 [-Wimplicit-function-declaration]
if (!log_table) make_log_table();
^
weibull.c:665:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
make_log_table()
^
17 warnings and 3 errors generated.
make: *** [weibull.o] Error 1
Maybe someone of you has any idea, what the problem could be???
I would be very glad for every answer :)
weibull.c:88:5: error: non-void function 'update_hist' should return a value [-Wreturn-type]
return;
^
weibull.c:92:5: error: non-void function 'update_hist' should return a value [-Wreturn-type]
return;
^
and
weibull.c:111:34: error: non-void function 'prune_hist' should return a value [-Wreturn-type]
if (reject_entry(score_entry)) return;
^
must return a vaule of type in given function's header.
I found a solution. The problem was, as I already feared, the compiler.
I installed a relatively new version (gcc 4.9), set this version as active and added the path in ~/.bash_profile (that was the most important step). Furthermore, I adopted the makefile. Opening a new terminal and typing "make" runs without errors.

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