=> Bootstrap dependency digest>=20211023: found digest-20211023
===> 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 primer3-2.3.6
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2  primer3_boulder_main.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2  -o format_output.o format_output.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2  -o read_boulder.o read_boulder.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2  -o print_boulder.o print_boulder.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -Wno-deprecated  -o libprimer3.o libprimer3.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o p3_seq_lib.o p3_seq_lib.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2  -o dpal_primer.o dpal.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -ffloat-store  -o thal_primer.o thal.c
dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)':
dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
     ^~~
dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
                                                      ^~~~~~~
thal.c: In function 'void thal(const unsigned char*, const unsigned char*, const thal_args*, thal_results*)':
thal.c:426:16: warning: comparison between pointer and zero character constant [-Wpointer-compare]
    if ('\0' == oligo_f) {
                ^~~~~~~
thal.c:426:16: note: did you mean to dereference the pointer?
thal.c:431:16: warning: comparison between pointer and zero character constant [-Wpointer-compare]
    if ('\0' == oligo_r) {
                ^~~~~~~
thal.c:431:16: note: did you mean to dereference the pointer?
thal.c: In function 'void tableStartATS(double, double (*)[5])':
thal.c:1198:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1201:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpS[0][3] = atpS[3][0] = atp_value;
      ^~~~
thal.c: In function 'void tableStartATH(double, double (*)[5])':
thal.c:1210:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1214:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpH[0][3] = atpH[3][0] = atp_value;
      ^~~~
gcc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2   -c -o oligotm.o oligotm.c
oligotm.c: In function 'oligotm':
oligotm.c:424:44: warning: comparison between pointer and zero character constant [-Wpointer-compare]
      for(i = 0; i <= len && d != NULL && d != '\0';) {
                                            ^~
oligotm.c:424:42: note: did you mean to dereference the pointer?
      for(i = 0; i <= len && d != NULL && d != '\0';) {
                                          ^
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c
ntdpal_main.c: In function 'int main(int, const char**)':
ntdpal_main.c:49:9: warning: variable 'tmp_ret' set but not used [-Wunused-but-set-variable]
     int tmp_ret;
         ^~~~~~~
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o dpal.o dpal.c
dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)':
dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
     ^~~
dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
                                                      ^~~~~~~
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o thal_main.o thal_main.c
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -ffloat-store -o thal.o thal.c
thal.c: In function 'void thal(const unsigned char*, const unsigned char*, const thal_args*, thal_results*)':
thal.c:426:16: warning: comparison between pointer and zero character constant [-Wpointer-compare]
    if ('\0' == oligo_f) {
                ^~~~~~~
thal.c:426:16: note: did you mean to dereference the pointer?
thal.c:431:16: warning: comparison between pointer and zero character constant [-Wpointer-compare]
    if ('\0' == oligo_r) {
                ^~~~~~~
thal.c:431:16: note: did you mean to dereference the pointer?
thal.c: In function 'void tableStartATS(double, double (*)[5])':
thal.c:1198:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1201:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpS[0][3] = atpS[3][0] = atp_value;
      ^~~~
thal.c: In function 'void tableStartATH(double, double (*)[5])':
thal.c:1210:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1214:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpH[0][3] = atpH[3][0] = atp_value;
      ^~~~
g++ -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o  -lm
ar rv libdpal.a dpal_primer.o
ar: creating libdpal.a
a - dpal_primer.o
ranlib libdpal.a
ar rv libthal.a thal_primer.o
ar rv liboligotm.a oligotm.o
ar: creating libthal.a
a - thal_primer.o
ar: ranlib libthal.a
creating liboligotm.a
a - oligotm.o
ranlib liboligotm.a
g++ -g -o ntdpal ntdpal_main.o dpal.o
g++ -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o oligotm oligotm_main.c liboligotm.a  -lm
ar rv libprimer3.a libprimer3.o p3_seq_lib.o
ar: creating libprimer3.a
a - libprimer3.o
a - p3_seq_lib.o
ranlib libprimer3.a
g++ -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o  libprimer3.a libdpal.a libthal.a liboligotm.a   -lm
g++ -g -o ntthal thal_main.o thal.o -lm