===> Building for primer3-2.3.6 g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 primer3_boulder_main.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o format_output.o format_output.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] if (pa->pick_left_primer && &retval->fwd != NULL ~~~~~~~~^~~ ~~~~ format_output.c:851:45: 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. g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o read_boulder.o read_boulder.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o print_boulder.o print_boulder.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] print_boulder.c:234:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(suffix, "_%d", i); ^ /Applications/Xcode-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Applications/Xcode-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. 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 clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating archive libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -o dpal_primer.o dpal.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ar rv libdpal.a dpal_primer.o ar: creating archive libdpal.a a - dpal_primer.o ranlib libdpal.a 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: optimization flag '-ffloat-store' is not supported [-Wignored-optimization-argument] 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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __x) _NOEXCEPT { ^ thal.c:772:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] THAL_IO_ERROR(paramdir); ^ thal.c:88:28: note: expanded from macro 'THAL_IO_ERROR' #define THAL_IO_ERROR(f) { sprintf(o->msg, "Unable to open file %s", f); longjmp(_jmp_buf, 1); } ^ /Applications/Xcode-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Applications/Xcode-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __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-15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk/usr/include/c++/v1/math.h:403:80: note: 'isfinite' declared here _LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isfinite(_A1 __x) _NOEXCEPT { ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 1 warning and 20 errors generated. gmake: *** [Makefile:192: thal_primer.o] Error 1 *** Error code 2 Stop. bmake[1]: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/primer3 *** Error code 1 Stop. bmake: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/primer3