=> Bootstrap dependency digest>=20211023: found digest-20211023
WARNING: [license.mk] Every package should define a LICENSE.
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Building for gp-0.26
--- all ---
cd src ; make PROGRAMS="gp_acc gp_cusage gp_digest gp_dimer gp_findorf gp_gc gp_getseq gp_matrix gp_mkmtx gp_pars gp_pattern gp_qs gp_randseq gp_scan gp_seq2prot gp_shift gp_slen gp_tm gp_trimer gp_primer gp_adjust gp_cdndev" GDPROGRAMS="" CC=gcc  LIBS=" -lm" CFLAGS="-pedantic -O3 -Wall -g" ;
--- genpak.o ---
gcc -pedantic -O3 -Wall -g   -c genpak.c
--- gp_acc ---
--- gp_cusage ---
--- gp_digest ---
--- gp_dimer ---
--- gp_cusage ---
Creating gp_cusage
gcc -pedantic -O3 -Wall -g -o gp_cusage genpak.o gp_cusage.c -lm
--- gp_digest ---
Creating gp_digest
gcc -pedantic -O3 -Wall -g -o gp_digest genpak.o gp_digest.c -lm
--- gp_acc ---
Creating gp_acc
gcc -pedantic -O3 -Wall -g -o gp_acc genpak.o gp_acc.c -lm
--- gp_dimer ---
Creating gp_dimer
gcc -pedantic -O3 -Wall -g -o gp_dimer genpak.o gp_dimer.c -lm
--- gp_cusage ---
gp_cusage.c: In function 'CountCodons':
gp_cusage.c:198:46: warning: array subscript has type 'char' [-Wchar-subscripts]
  for(i = 0,j = 0;i<3;i++,j++) coord[i] = Conv[inseq->sequ[j]] ;
                                              ^
--- gp_acc ---
gp_acc.c: In function 'main':
gp_acc.c:64:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_acc.c:59:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_acc.c:56:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
--- gp_cusage ---
gp_cusage.c:215:24: warning: array subscript has type 'char' [-Wchar-subscripts]
    else coord[i] = Conv[inseq->sequ[j]] ;
                        ^
gp_cusage.c:185:11: warning: unused variable 'tmp' [-Wunused-variable]
  char t, *tmp;
           ^~~
gp_cusage.c: In function 'ReadCodonTable':
gp_cusage.c:280:11: warning: array subscript has type 'char' [-Wchar-subscripts]
    if(Conv[t] > 3 || Conv[t] < 0) {
           ^
gp_cusage.c:280:26: warning: array subscript has type 'char' [-Wchar-subscripts]
    if(Conv[t] > 3 || Conv[t] < 0) {
                          ^
gp_cusage.c:283:20: warning: array subscript has type 'char' [-Wchar-subscripts]
     coord[i] = Conv[t] ;
                    ^
gp_cusage.c:295:17: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                 ^
gp_cusage.c:295:27: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                           ^
gp_cusage.c:295:37: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                                     ^
--- gp_acc ---
gp_acc.c: In function 'FormatHeader':
gp_acc.c:289:23: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
     fprintf(o.out,"z(%i)z(%i)L(%i)\t",i,k,j) ;
                      ~^
                      %li
gp_acc.c:289:28: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
     fprintf(o.out,"z(%i)z(%i)L(%i)\t",i,k,j) ;
                           ~^
                           %li
gp_acc.c:289:33: warning: format '%i' expects argument of type 'int', but argument 5 has type 'long int' [-Wformat=]
     fprintf(o.out,"z(%i)z(%i)L(%i)\t",i,k,j) ;
                                ~^
                                %li
--- gp_cusage ---
gp_cusage.c: In function 'PrintCodonUsageTable':
gp_cusage.c:332:16: warning: array subscript has type 'char' [-Wchar-subscripts]
       one2three[cdtable->tbl[i][j][k]]) ;
                ^
gp_cusage.c:368:18: warning: array subscript has type 'char' [-Wchar-subscripts]
         one2three[cdtable->tbl[i][j][k]],
                  ^
gp_cusage.c:414:18: warning: array subscript has type 'char' [-Wchar-subscripts]
         one2three[cdtable->tbl[i][j][k]],
                  ^
--- gp_digest ---
gp_digest.c: In function 'main':
gp_digest.c:72:26: warning: variable 'altenzfile' set but not used [-Wunused-but-set-variable]
  int c,show_info = FALSE,altenzfile = FALSE;
                          ^~~~~~~~~~
gp_digest.c:64:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
--- gp_cusage ---
gp_cusage.c: In function 'PrintCodonTable':
gp_cusage.c:489:18: warning: array subscript has type 'char' [-Wchar-subscripts]
         one2three[intable->tbl[i][j][k]]) ;
                  ^
--- gp_digest ---
gp_digest.c: In function 'FindRestrictionSites':
gp_digest.c:211:19: warning: implicit declaration of function 'Compare' [-Wimplicit-function-declaration]
   while(j<dl_e && Compare(s->sequ[i+j],e->sequ[j]) ) j++;
                   ^~~~~~~
gp_digest.c:197:10: warning: unused variable 'width' [-Wunused-variable]
  int i,j,width = 70 ;
          ^~~~~
--- gp_dimer ---
gp_dimer.c: In function 'main':
gp_dimer.c:109:2: warning: implicit declaration of function 'PrintHeader'; did you mean 'PrintFtable'? [-Wimplicit-function-declaration]
  PrintHeader(options) ;
  ^~~~~~~~~~~
  PrintFtable
gp_dimer.c:57:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_dimer.c:53:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_dimer.c:51:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
gp_dimer.c: In function 'GetFtable':
gp_dimer.c:219:8: warning: array subscript has type 'char' [-Wchar-subscripts]
   i = C[c1] ; j = C[c2] ;
        ^
gp_dimer.c:219:20: warning: array subscript has type 'char' [-Wchar-subscripts]
   i = C[c1] ; j = C[c2] ;
                    ^
--- gp_findorf ---
Creating gp_findorf
gcc -pedantic -O3 -Wall -g -o gp_findorf genpak.o gp_findorf.c -lm
--- gp_gc ---
Creating gp_gc
gcc -pedantic -O3 -Wall -g -o gp_gc genpak.o gp_gc.c -lm
--- gp_findorf ---
gp_findorf.c: In function 'main':
gp_findorf.c:93:14: warning: implicit declaration of function 'getopt'; did you mean 'gp_getopt'? [-Wimplicit-function-declaration]
  while ((c = getopt(argc, argv, "o:m:M:pc:vHhqd")) != EOF)
              ^~~~~~
              gp_getopt
gp_findorf.c:68:6: warning: variable 'optionaltable' set but not used [-Wunused-but-set-variable]
  int optionaltable = FALSE ;
      ^~~~~~~~~~~~~
gp_findorf.c: In function 'ExtractOrfs':
gp_findorf.c:227:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ;
      ^~~~~
gp_findorf.c: In function 'ReadCodonTable':
gp_findorf.c:323:11: warning: array subscript has type 'char' [-Wchar-subscripts]
    if(Conv[t] > 3 || Conv[t] < 0) {
           ^
gp_findorf.c:323:26: warning: array subscript has type 'char' [-Wchar-subscripts]
    if(Conv[t] > 3 || Conv[t] < 0) {
                          ^
gp_findorf.c:326:20: warning: array subscript has type 'char' [-Wchar-subscripts]
     coord[i] = Conv[t] ;
                    ^
gp_findorf.c:338:17: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                 ^
gp_findorf.c:338:27: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                           ^
gp_findorf.c:338:37: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                                     ^
gp_findorf.c: In function 'PrintCodonTable':
gp_findorf.c:407:18: warning: array subscript has type 'char' [-Wchar-subscripts]
         one2three[intable->tbl[i][j][k]]) ;
                  ^
--- gp_getseq ---
Creating gp_getseq
gcc -pedantic -O3 -Wall -g -o gp_getseq genpak.o gp_getseq.c -lm
--- gp_cusage ---
gp_cusage.c: In function 'main':
gp_cusage.c:155:7: warning: 'in' may be used uninitialized in this function [-Wmaybe-uninitialized]
  while( (inseq = gp_seq_read_fragment(in,0,0,0)) != NULL) {
       ^
--- gp_getseq ---
gp_getseq.c: In function 'main':
gp_getseq.c:80:27: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
    if(optarg[0] == '-' && strlen(optarg) == 1) {
                           ^~~~~~
gp_getseq.c:80:27: warning: incompatible implicit declaration of built-in function 'strlen'
gp_getseq.c:80:27: note: include '<string.h>' or provide a declaration of 'strlen'
--- gp_gc ---
gp_gc.c: In function 'GCDistro':
gp_gc.c:172:7: warning: array subscript has type 'char' [-Wchar-subscripts]
    cnv[c]++ ;
       ^
gp_gc.c: In function 'ComputateGC':
gp_gc.c:194:12: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
  dlugosc = strlen(s->sequ) ;
            ^~~~~~
gp_gc.c:194:12: warning: incompatible implicit declaration of built-in function 'strlen'
gp_gc.c:194:12: note: include '<string.h>' or provide a declaration of 'strlen'
gp_gc.c:198:6: warning: array subscript has type 'char' [-Wchar-subscripts]
   cnv[c]++ ;
      ^
--- gp_matrix ---
Creating gp_matrix
gcc -pedantic -O3 -Wall -g -o gp_matrix genpak.o gp_matrix.c -lm
--- gp_mkmtx ---
--- gp_matrix ---
gp_matrix.c: In function 'EvaluateSequence':
gp_matrix.c:556:15: warning: array subscript has type 'char' [-Wchar-subscripts]
      index = c[s->sequ[pos]] ;
               ^
gp_matrix.c:565:15: warning: array subscript has type 'char' [-Wchar-subscripts]
      index = c[s->sequ[pos]] ;
               ^
gp_matrix.c:574:15: warning: array subscript has type 'char' [-Wchar-subscripts]
      index = c[s->sequ[pos]] ;
               ^
gp_matrix.c:606:2: warning: implicit declaration of function 'strcpy' [-Wimplicit-function-declaration]
  strcpy(res->name,s->name) ;
  ^~~~~~
gp_matrix.c:606:2: warning: incompatible implicit declaration of built-in function 'strcpy'
gp_matrix.c:606:2: note: include '<string.h>' or provide a declaration of 'strcpy'
--- gp_mkmtx ---
Creating gp_mkmtx
gcc -pedantic -O3 -Wall -g -o gp_mkmtx genpak.o gp_mkmtx.c -lm
--- gp_matrix ---
gp_matrix.c:630:15: warning: array subscript has type 'char' [-Wchar-subscripts]
   om->m35[i][c[s->sequ[(res->pos + i)]]] += 1 ;
               ^
gp_matrix.c:633:15: warning: array subscript has type 'char' [-Wchar-subscripts]
   om->m10[i][c[s->sequ[(res->pos + m35_size + res->gap10 + i)]]] += 1 ;
               ^
gp_matrix.c:637:14: warning: array subscript has type 'char' [-Wchar-subscripts]
   om->m1[i][c[s->sequ[(blocksize + i)]]] += 1 ;
              ^
gp_matrix.c: In function 'GetGCDistro':
gp_matrix.c:845:11: warning: unused variable 'gc' [-Wunused-variable]
  double t,gc ;
           ^~
--- gp_pars ---
--- gp_matrix ---
gp_matrix.c: In function 'PrintPromoter':
gp_matrix.c:1017:3: warning: incompatible implicit declaration of built-in function 'strcpy'
   strcpy(s1,"</TD><TD BGCOLOR= \"yellow\"><B>") ;
   ^~~~~~
gp_matrix.c:1017:3: note: include '<string.h>' or provide a declaration of 'strcpy'
gp_matrix.c:1021:3: warning: incompatible implicit declaration of built-in function 'strcpy'
   strcpy(s1,"[") ;
   ^~~~~~
gp_matrix.c:1021:3: note: include '<string.h>' or provide a declaration of 'strcpy'
gp_matrix.c:1034:14: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
  for(i = 0;i<strlen(prom->sequ);i++){
              ^~~~~~
gp_matrix.c:1034:14: warning: incompatible implicit declaration of built-in function 'strlen'
gp_matrix.c:1034:14: note: include '<string.h>' or provide a declaration of 'strlen'
--- gp_pars ---
Creating gp_pars
gcc -pedantic -O3 -Wall -g -o gp_pars genpak.o gp_pars.c -lm
--- gp_pattern ---
Creating gp_pattern
gcc -pedantic -O3 -Wall -g -o gp_pattern genpak.o gp_pattern.c -lm
--- gp_mkmtx ---
gp_mkmtx.c: In function 'GetMatrix':
gp_mkmtx.c:215:12: warning: array subscript has type 'char' [-Wchar-subscripts]
     t[i*4+C[c]] += 1 ;
            ^
--- gp_pars ---
gp_pars.c: In function 'main':
gp_pars.c:39:15: warning: unused variable 'optarg' [-Wunused-variable]
  extern char *optarg ;
               ^~~~~~
gp_pars.c:38:13: warning: unused variable 'optind' [-Wunused-variable]
  extern int optind ;
             ^~~~~~
--- gp_pattern ---
gp_pattern.c: In function 'main':
gp_pattern.c:128:2: warning: implicit declaration of function 'PrintHead' [-Wimplicit-function-declaration]
  PrintHead(options) ;
  ^~~~~~~~~
gp_pattern.c:133:3: warning: implicit declaration of function 'GetFreq' [-Wimplicit-function-declaration]
   GetFreq(tablica,options,inseq) ;
   ^~~~~~~
gp_pattern.c:134:3: warning: implicit declaration of function 'PrintFreq' [-Wimplicit-function-declaration]
   PrintFreq(tablica,options,inseq) ;
   ^~~~~~~~~
gp_pattern.c:72:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_pattern.c:71:10: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k,c;
          ^
gp_pattern.c:71:8: warning: unused variable 'j' [-Wunused-variable]
  int i,j,k,c;
        ^
gp_pattern.c:67:6: warning: unused variable 'crd' [-Wunused-variable]
  int crd[3] = {2,2,2} ;
      ^~~
gp_pattern.c:66:6: warning: unused variable 'ndim' [-Wunused-variable]
  int ndim = 3 ;
      ^~~~
gp_pattern.c:64:11: warning: unused variable 'ftable' [-Wunused-variable]
  double **ftable ; /* here we store the frequencies */
           ^~~~~~
gp_pattern.c:63:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_pattern.c:61:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
gp_pattern.c: In function 'GetFreq':
gp_pattern.c:146:10: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k ;
          ^
gp_pattern.c: In function 'PrintFreq':
gp_pattern.c:214:7: warning: unused variable 'crd' [-Wunused-variable]
  int *crd ;
       ^~~
gp_pattern.c:212:10: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k ;
          ^
gp_pattern.c:212:8: warning: unused variable 'j' [-Wunused-variable]
  int i,j,k ;
        ^
gp_pattern.c: In function 'gp_elpos':
gp_pattern.c:270:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
   fprintf(stderr," position %i\n",p) ;
                             ~^
                             %li
gp_pattern.c:259:11: warning: unused variable 'k' [-Wunused-variable]
  long i,j,k,p = 0,sum = 1 ;
           ^
gp_pattern.c:259:9: warning: unused variable 'j' [-Wunused-variable]
  long i,j,k,p = 0,sum = 1 ;
         ^
gp_pattern.c: In function 'gp_getel':
gp_pattern.c:280:15: warning: unused variable 'sum' [-Wunused-variable]
  long i,j,k,p,sum ;
               ^~~
gp_pattern.c:280:11: warning: unused variable 'k' [-Wunused-variable]
  long i,j,k,p,sum ;
           ^
gp_pattern.c:280:9: warning: unused variable 'j' [-Wunused-variable]
  long i,j,k,p,sum ;
         ^
gp_pattern.c:280:7: warning: unused variable 'i' [-Wunused-variable]
  long i,j,k,p,sum ;
       ^
gp_pattern.c: In function 'gp_putel':
gp_pattern.c:291:15: warning: unused variable 'sum' [-Wunused-variable]
  long i,j,k,p,sum ;
               ^~~
gp_pattern.c:291:11: warning: unused variable 'k' [-Wunused-variable]
  long i,j,k,p,sum ;
           ^
gp_pattern.c:291:9: warning: unused variable 'j' [-Wunused-variable]
  long i,j,k,p,sum ;
         ^
gp_pattern.c:291:7: warning: unused variable 'i' [-Wunused-variable]
  long i,j,k,p,sum ;
       ^
gp_pattern.c: In function 'gp_zerot':
gp_pattern.c:304:19: warning: unused variable 'k' [-Wunused-variable]
  long sum = 1,i,j,k ;
                   ^
gp_pattern.c:304:17: warning: unused variable 'j' [-Wunused-variable]
  long sum = 1,i,j,k ;
                 ^
gp_pattern.c: In function 'PrintNuc':
gp_pattern.c:188:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
--- gp_qs ---
Creating gp_qs
gcc -pedantic -O3 -Wall -g -o gp_qs genpak.o gp_qs.c -lm
gp_qs.c: In function 'main':
gp_qs.c:121:25: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
   needle->sequ = calloc(strlen(argv[optind]) + 1, sizeof(*needle->sequ)) ;
                         ^~~~~~
gp_qs.c:121:25: warning: incompatible implicit declaration of built-in function 'strlen'
gp_qs.c:121:25: note: include '<string.h>' or provide a declaration of 'strlen'
gp_qs.c:122:3: warning: implicit declaration of function 'strcpy' [-Wimplicit-function-declaration]
   strcpy(needle->sequ,argv[optind]) ;
   ^~~~~~
gp_qs.c:122:3: warning: incompatible implicit declaration of built-in function 'strcpy'
gp_qs.c:122:3: note: include '<string.h>' or provide a declaration of 'strcpy'
gp_qs.c:55:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_qs.c:54:17: warning: unused variable 'needle_stdin' [-Wunused-variable]
  int c, nmatch, needle_stdin = FALSE;
                 ^~~~~~~~~~~~
gp_qs.c: In function 'degenerate_sequence':
gp_qs.c:192:6: warning: incompatible implicit declaration of built-in function 'strlen'
  l = strlen(n->sequ) ;
      ^~~~~~
gp_qs.c:192:6: note: include '<string.h>' or provide a declaration of 'strlen'
gp_qs.c: In function 'SearchNeedle':
gp_qs.c:218:2: warning: implicit declaration of function 'strcat' [-Wimplicit-function-declaration]
  strcat(name," v. ") ;
  ^~~~~~
gp_qs.c:218:2: warning: incompatible implicit declaration of built-in function 'strcat'
gp_qs.c:218:2: note: include '<string.h>' or provide a declaration of 'strcat'
gp_qs.c:220:6: warning: incompatible implicit declaration of built-in function 'strlen'
  j = strlen(name) ;
      ^~~~~~
gp_qs.c:220:6: note: include '<string.h>' or provide a declaration of 'strlen'
gp_qs.c:241:16: warning: implicit declaration of function 'Compare' [-Wimplicit-function-declaration]
     i < dln && Compare(n->sequ[i], s->sequ[pos1+i]) ;
                ^~~~~~~
--- gp_randseq ---
Creating gp_randseq
gcc -pedantic -O3 -Wall -g -o gp_randseq genpak.o gp_randseq.c -lm
--- gp_qs ---
gp_qs.c:221:2: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
  for(i = j;i<(j+10);i++) {
  ^~~
--- gp_randseq ---
gp_randseq.c: In function 'main':
gp_randseq.c:133:12: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
  dlugosc = strlen(Rezultat->sequ) ;
            ^~~~~~
gp_randseq.c:133:12: warning: incompatible implicit declaration of built-in function 'strlen'
gp_randseq.c:133:12: note: include '<string.h>' or provide a declaration of 'strlen'
--- gp_qs ---
gp_qs.c: In function 'main':
gp_qs.c:177:12: warning: 'nmatch' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(debug) gp_warn("%i matches found",nmatch) ;
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gp_qs.c:171:11: warning: 'needle' may be used uninitialized in this function [-Wmaybe-uninitialized]
    nmatch = SearchNeedle(inseq, needle, opt) ;
    ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--- gp_scan ---
--- gp_seq2prot ---
Creating gp_seq2prot
gcc -pedantic -O3 -Wall -g -o gp_seq2prot genpak.o gp_seq2prot.c -lm
--- gp_scan ---
Creating gp_scan
gcc -pedantic -O3 -Wall -g -o gp_scan genpak.o gp_scan.c -lm
--- gp_shift ---
Creating gp_shift
gcc -pedantic -O3 -Wall -g -o gp_shift genpak.o gp_shift.c -lm
--- gp_scan ---
gp_scan.c: In function 'main':
gp_scan.c:61:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_scan.c:58:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_scan.c:55:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
gp_scan.c: In function 'ScanSeq':
--- gp_seq2prot ---
gp_seq2prot.c: In function 'main':
--- gp_scan ---
gp_scan.c:203:6: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
  l = strlen(s->sequ) ;
      ^~~~~~
--- gp_seq2prot ---
gp_seq2prot.c:52:6: warning: variable 'optionaltable' set but not used [-Wunused-but-set-variable]
  int optionaltable = FALSE ;
      ^~~~~~~~~~~~~
gp_seq2prot.c:50:6: warning: unused variable 'check' [-Wunused-variable]
  int check = TRUE ;
      ^~~~~
--- gp_scan ---
gp_scan.c:203:6: warning: incompatible implicit declaration of built-in function 'strlen'
gp_scan.c:203:6: note: include '<string.h>' or provide a declaration of 'strlen'
--- gp_seq2prot ---
gp_seq2prot.c: In function 'ReadCodonTable':
gp_seq2prot.c:200:11: warning: array subscript has type 'char' [-Wchar-subscripts]
    if(Conv[t] > 3 || Conv[t] < 0) {
           ^
gp_seq2prot.c:200:26: warning: array subscript has type 'char' [-Wchar-subscripts]
    if(Conv[t] > 3 || Conv[t] < 0) {
                          ^
gp_seq2prot.c:203:20: warning: array subscript has type 'char' [-Wchar-subscripts]
     coord[i] = Conv[t] ;
                    ^
gp_seq2prot.c:215:17: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                 ^
gp_seq2prot.c:215:27: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                           ^
gp_seq2prot.c:215:37: warning: array subscript has type 'char' [-Wchar-subscripts]
    outtable->tbl[coord[0]][coord[1]][coord[2]] = t ;
                                     ^
--- gp_scan ---
gp_scan.c:199:11: warning: unused variable 'k' [-Wunused-variable]
  long i,j,k,l,c1,c2 ;
           ^
--- gp_seq2prot ---
gp_seq2prot.c: In function 'PrintCodonTable':
gp_seq2prot.c:282:18: warning: array subscript has type 'char' [-Wchar-subscripts]
         one2three[intable->tbl[i][j][k]]) ;
                  ^
--- gp_shift ---
gp_shift.c: In function 'main':
gp_shift.c:118:2: warning: implicit declaration of function 'shift_positions' [-Wimplicit-function-declaration]
  shift_positions(opt) ;
  ^~~~~~~~~~~~~~~
gp_shift.c:49:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_shift.c:49:8: warning: unused variable 'inseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
        ^~~~~
gp_shift.c:47:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
gp_shift.c:46:15: warning: unused variable 'optarg' [-Wunused-variable]
  extern char *optarg ;
               ^~~~~~
gp_shift.c: In function 'shift_positions':
gp_shift.c:163:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
   fprintf(o.out,"%i %i",ss,ee) ;
                  ~^
                  %li
gp_shift.c:163:22: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
   fprintf(o.out,"%i %i",ss,ee) ;
                     ~^
                     %li
gp_shift.c:131:6: warning: unused variable 'res' [-Wunused-variable]
  int res = 0, line = 0;
      ^~~
--- gp_slen ---
Creating gp_slen
gcc -pedantic -O3 -Wall -g -o gp_slen genpak.o gp_slen.c -lm
gp_slen.c: In function 'main':
gp_slen.c:97:39: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
   if(onlymean == FALSE) fprintf(out,"%i\n",dlug) ;
                                      ~^
                                      %li
--- gp_tm ---
--- gp_trimer ---
Creating gp_trimer
gcc -pedantic -O3 -Wall -g -o gp_trimer genpak.o gp_trimer.c -lm
--- gp_tm ---
Creating gp_tm
gcc -pedantic -O3 -Wall -g -o gp_tm genpak.o gp_tm.c -lm
--- gp_trimer ---
gp_trimer.c: In function 'main':
gp_trimer.c:101:2: warning: implicit declaration of function 'PrintHeader'; did you mean 'PrintFtable'? [-Wimplicit-function-declaration]
  PrintHeader(options) ;
  ^~~~~~~~~~~
  PrintFtable
gp_trimer.c:56:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_trimer.c:52:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_trimer.c:50:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
gp_trimer.c:49:15: warning: unused variable 'optarg' [-Wunused-variable]
  extern char *optarg ;
               ^~~~~~
gp_trimer.c: In function 'GetFtable':
gp_trimer.c:211:8: warning: array subscript has type 'char' [-Wchar-subscripts]
   i = C[c1] ; j = C[c2] ; k = C[c3] ;
        ^
gp_trimer.c:211:20: warning: array subscript has type 'char' [-Wchar-subscripts]
   i = C[c1] ; j = C[c2] ; k = C[c3] ;
                    ^
gp_trimer.c:211:32: warning: array subscript has type 'char' [-Wchar-subscripts]
   i = C[c1] ; j = C[c2] ; k = C[c3] ;
                                ^
--- gp_tm ---
gp_tm.c: In function 'main':
gp_tm.c:70:13: warning: unused variable 'dg' [-Wunused-variable]
  double dh, dg, ds ;
             ^~
gp_tm.c:66:9: warning: variable 'onlymean' set but not used [-Wunused-but-set-variable]
  int c, onlymean = FALSE  ;
         ^~~~~~~~
gp_tm.c: In function 'CompParam':
gp_tm.c:214:26: warning: array subscript has type 'char' [-Wchar-subscripts]
   result += DP.seqpar[cnv[cx]][cnv[cy]] ;
                          ^
gp_tm.c:214:35: warning: array subscript has type 'char' [-Wchar-subscripts]
   result += DP.seqpar[cnv[cx]][cnv[cy]] ;
                                   ^
--- gp_primer ---
Creating gp_primer
gcc -pedantic -O3 -Wall -g -o gp_primer genpak.o gp_primer.c -lm
gp_primer.c: In function 'main':
gp_primer.c:87:7: warning: unused variable 'message' [-Wunused-variable]
  char message[100] ;
       ^~~~~~~
gp_primer.c:83:16: warning: unused variable 'outseq' [-Wunused-variable]
  sekw *inseq, *outseq ;
                ^~~~~~
gp_primer.c:81:6: warning: unused variable 'width' [-Wunused-variable]
  int width = 70 ; /* width with which the sequence gets formatted */
      ^~~~~
gp_primer.c: In function 'dimer_find':
gp_primer.c:215:7: warning: implicit declaration of function 'Compare' [-Wimplicit-function-declaration]
    if(Compare(*p, *q)) {
       ^~~~~~~
gp_primer.c:217:33: warning: array subscript has type 'char' [-Wchar-subscripts]
      dimeres[i].energy += dg[cnv[*(p - 1)]][cnv[*p]] ;
                                 ^
gp_primer.c:217:48: warning: array subscript has type 'char' [-Wchar-subscripts]
      dimeres[i].energy += dg[cnv[*(p - 1)]][cnv[*p]] ;
                                                ^
gp_primer.c:233:4: warning: implicit declaration of function 'dimer_print'; did you mean 'dimer_find'? [-Wimplicit-function-declaration]
    dimer_print(s, &dimeres[i], o) ;
    ^~~~~~~~~~~
    dimer_find
gp_primer.c:193:10: warning: unused variable 'd' [-Wunused-variable]
  char c, d, *shift, *p, *q ;
          ^
gp_primer.c:193:7: warning: unused variable 'c' [-Wunused-variable]
  char c, d, *shift, *p, *q ;
       ^
gp_primer.c: In function 'dimer_print':
gp_primer.c:246:11: warning: unused variable 'p' [-Wunused-variable]
  char c, *p ;
           ^
gp_primer.c: In function 'stem_find':
gp_primer.c:314:4: warning: implicit declaration of function 'stem_print'; did you mean 'stem_find'? [-Wimplicit-function-declaration]
    stem_print(s, &stems[i], o) ;
    ^~~~~~~~~~
    stem_find
gp_primer.c:271:9: warning: unused variable 'j' [-Wunused-variable]
  int i, j, maxstruct, maxloop ;
         ^
gp_primer.c: In function 'stem_energy':
gp_primer.c:361:18: warning: array subscript has type 'char' [-Wchar-subscripts]
     res += dg[cnv[d]][cnv[c]] ;
                  ^
gp_primer.c:361:26: warning: array subscript has type 'char' [-Wchar-subscripts]
     res += dg[cnv[d]][cnv[c]] ;
                          ^
gp_primer.c:341:6: warning: unused variable 'i' [-Wunused-variable]
  int i, j, last ;
      ^
gp_primer.c:340:6: warning: unused variable 'onlyAT' [-Wunused-variable]
  int onlyAT = TRUE ;
      ^~~~~~
gp_primer.c:337:20: warning: unused variable 'tmp' [-Wunused-variable]
  double res = 0.0, tmp ;
                    ^~~
gp_primer.c: In function 'stem_print':
gp_primer.c:399:18: warning: unused variable 'sp' [-Wunused-variable]
  char c, *p, *q, sp[101] ;
                  ^~
gp_primer.c:398:19: warning: unused variable 'k' [-Wunused-variable]
  int l, ls, i, j, k ;
                   ^
gp_primer.c:398:16: warning: unused variable 'j' [-Wunused-variable]
  int l, ls, i, j, k ;
                ^
gp_primer.c:398:9: warning: unused variable 'ls' [-Wunused-variable]
  int l, ls, i, j, k ;
         ^~
--- gp_adjust ---
Creating gp_adjust
gcc -pedantic -O3 -Wall -g -o gp_adjust genpak.o gp_adjust.c -lm
--- gp_cdndev ---
Creating gp_cdndev
gcc -pedantic -O3 -Wall -g -o gp_cdndev genpak.o gp_cdndev.c -lm
--- gp_primer ---
gp_primer.c: In function 'main':
gp_primer.c:175:22: warning: 'stem' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if(options.stems) fprintf(options.out, "%.2f\t", stem) ;
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gp_primer.c:174:24: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if(options.dimeres) fprintf(options.out, "%.2f\t", dim) ;
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

All programs compiled. 
Type 'make install' to install all programs.