=> Bootstrap dependency digest>=20211023: found digest-20220214
===> 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]
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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: 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-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/math.h:452:1: note: 'isfinite' declared here
isfinite(_A1 __lcpp_x) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake: *** [Makefile:192: thal_primer.o] Error 1
*** Error code 2
Stop.
bmake[1]: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/primer3
*** Error code 1
Stop.
bmake: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/primer3