=> "/opt/pkg/bin/bmake" ["-C", "/Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/primer3", "all", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] ===> 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 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] format_output.c:418:48: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] 418 | 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] 429 | 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] 851 | 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] 858 | 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] 865 | 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] 888 | 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] 907 | 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] 926 | 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 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] 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] 234 | sprintf(suffix, "_%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __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-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #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] 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] 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'? 523 | if(isFinite(mh)) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:593:12: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 593 | if (!isFinite(SHleft)) bestI = bestJ = 1; | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:603:10: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 603 | if(isFinite(EnthalpyDPT(bestI, bestJ))){ | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ 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] 772 | THAL_IO_ERROR(paramdir); | ^ thal.c:88:28: note: expanded from macro 'THAL_IO_ERROR' 88 | #define THAL_IO_ERROR(f) { sprintf(o->msg, "Unable to open file %s", f); longjmp(_jmp_buf, 1); } | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __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-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ thal.c:921:24: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 921 | if (!isFinite(stackEntropies[i][ii][j][jj]) || !isFinite(stackEnthalpies[i][ii][j][jj])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:921:67: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 921 | if (!isFinite(stackEntropies[i][ii][j][jj]) || !isFinite(stackEnthalpies[i][ii][j][jj])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:951:24: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 951 | if (!isFinite(stackint2Entropies[i][ii][j][jj]) || !isFinite(stackint2Enthalpies[i][ii][j][jj])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:951:71: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 951 | if (!isFinite(stackint2Entropies[i][ii][j][jj]) || !isFinite(stackint2Enthalpies[i][ii][j][jj])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1003:18: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1003 | if(!isFinite(dangleEntropies3[i][k][j]) || !isFinite(dangleEnthalpies3[i][k][j])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1003:58: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1003 | if(!isFinite(dangleEntropies3[i][k][j]) || !isFinite(dangleEnthalpies3[i][k][j])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1022:18: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1022 | if(!isFinite(dangleEntropies5[i][j][k]) || !isFinite(dangleEnthalpies5[i][j][k])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1022:58: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1022 | if(!isFinite(dangleEntropies5[i][j][k]) || !isFinite(dangleEnthalpies5[i][j][k])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1068:20: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1068 | if (!isFinite(tstackEntropies[i1][i2][j1][j2]) || !isFinite(tstackEnthalpies[i1][i2][j1][j2])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1068:66: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1068 | if (!isFinite(tstackEntropies[i1][i2][j1][j2]) || !isFinite(tstackEnthalpies[i1][i2][j1][j2])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1098:20: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1098 | if (!isFinite(tstack2Entropies[i1][i2][j1][j2]) || !isFinite(tstack2Enthalpies[i1][i2][j1][j2])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1098:67: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1098 | if (!isFinite(tstack2Entropies[i1][i2][j1][j2]) || !isFinite(tstack2Enthalpies[i1][i2][j1][j2])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1293:6: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1293 | if(isFinite(EnthalpyDPT(i, j))) { /* if finite */ | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1297:9: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1297 | if(isFinite(SH[1])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1311:12: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1311 | if (isFinite(EnthalpyDPT(ii, jj))) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ thal.c:1320:7: error: use of undeclared identifier 'finite'; did you mean 'isfinite'? 1320 | if(isFinite(SH[1])) { | ^ thal.c:104:22: note: expanded from macro 'isFinite' 104 | # define isFinite(x) finite(x) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/c++/v1/math.h:419:20: note: 'isfinite' declared here 419 | using std::__math::isfinite; | ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 1 warning and 20 errors generated. gmake: *** [Makefile:192: thal_primer.o] Error 1 gmake: *** Waiting for unfinished jobs.... *** 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