=> Bootstrap dependency digest>=20010302: found digest-20190127 ===> Skipping vulnerability checks. WARNING: No /opt/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/opt/pkg/sbin/pkg_admin -K /opt/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 clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: optimization flag '-ffloat-store' is not supported [-Wignored-optimization-argument] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] thal.c:523:10: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(isFinite(mh)) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:593:12: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(SHleft)) bestI = bestJ = 1; ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:603:10: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(isFinite(EnthalpyDPT(bestI, bestJ))){ ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:921:24: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(stackEntropies[i][ii][j][jj]) || !isFinite(stackEnthalpies[i][ii][j][jj])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:921:67: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(stackEntropies[i][ii][j][jj]) || !isFinite(stackEnthalpies[i][ii][j][jj])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:951:24: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(stackint2Entropies[i][ii][j][jj]) || !isFinite(stackint2Enthalpies[i][ii][j][jj])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:951:71: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(stackint2Entropies[i][ii][j][jj]) || !isFinite(stackint2Enthalpies[i][ii][j][jj])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1003:18: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(!isFinite(dangleEntropies3[i][k][j]) || !isFinite(dangleEnthalpies3[i][k][j])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1003:58: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(!isFinite(dangleEntropies3[i][k][j]) || !isFinite(dangleEnthalpies3[i][k][j])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1022:18: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(!isFinite(dangleEntropies5[i][j][k]) || !isFinite(dangleEnthalpies5[i][j][k])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1022:58: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(!isFinite(dangleEntropies5[i][j][k]) || !isFinite(dangleEnthalpies5[i][j][k])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1068:20: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(tstackEntropies[i1][i2][j1][j2]) || !isFinite(tstackEnthalpies[i1][i2][j1][j2])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1068:66: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(tstackEntropies[i1][i2][j1][j2]) || !isFinite(tstackEnthalpies[i1][i2][j1][j2])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1098:20: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(tstack2Entropies[i1][i2][j1][j2]) || !isFinite(tstack2Enthalpies[i1][i2][j1][j2])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1098:67: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (!isFinite(tstack2Entropies[i1][i2][j1][j2]) || !isFinite(tstack2Enthalpies[i1][i2][j1][j2])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1293:6: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(isFinite(EnthalpyDPT(i, j))) { /* if finite */ ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1297:9: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(isFinite(SH[1])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1311:12: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if (isFinite(EnthalpyDPT(ii, jj))) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ thal.c:1320:7: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? if(isFinite(SH[1])) { ^ thal.c:104:22: note: expanded from macro 'isFinite' # define isFinite(x) finite(x) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:441:1: note: 'isfinite' declared here isfinite(_A1 __lcpp_x) _NOEXCEPT ^ format_output.c:418:48: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (pa->pick_right_primer && &retval->rev != NULL ~~~~~~~~^~~ ~~~~ format_output.c:429:47: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare] fatal error: too many errors emitted, stopping now [-ferror-limit=] if (pa->pick_left_primer && &retval->fwd != NULL ~~~~~~~~^~~ ~~~~ 20 errors generated. format_output.c:851:45: gmake: *** [Makefile:192: thal_primer.o] Error 1 gmake: *** Waiting for unfinished jobs.... warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_left_primer) && (&retval->fwd != NULL ) ~~~~~~~~^~~ ~~~~ format_output.c:858:48: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) ~~~~~~~~^~~~ ~~~~ format_output.c:865:46: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_right_primer) && (&retval->rev != NULL ) ~~~~~~~~^~~ ~~~~ format_output.c:888:43: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_left_primer) && (&retval->fwd != NULL ) ~~~~~~~~^~~ ~~~~ format_output.c:907:46: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) ~~~~~~~~^~~~ ~~~~ format_output.c:926:44: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_right_primer) && (&retval->rev != NULL ) ~~~~~~~~^~~ ~~~~ 8 warnings generated. *** Error code 2 Stop. bmake[1]: stopped in /opt/pkgsrc/biology/primer3 *** Error code 1 Stop. bmake: stopped in /opt/pkgsrc/biology/primer3