hostname:  cluster038
[*] /tmp/biology/haplohseq/work/.tools/bin/mkdir -p build build/bin build/obj
[*] /tmp/biology/haplohseq/work/.tools/bin/mkdir -p build/test
<.> /bin/mkdir -p -p build build/bin build/obj
<.> /bin/mkdir -p -p build/test
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/InputProcessor.o src/util/InputProcessor.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/InputProcessor.o src/util/InputProcessor.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Reporter.o src/Reporter.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Reporter.o src/Reporter.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/FreqPhase.o src/FreqPhase.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/FreqPhase.o src/FreqPhase.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/VcfUtil.o src/util/VcfUtil.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/VcfUtil.o src/util/VcfUtil.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/HaplohSeq.o src/HaplohSeq.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/HaplohSeq.o src/HaplohSeq.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/FreqPhaseTest.o src/test/FreqPhaseTest.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/FreqPhaseTest.o src/test/FreqPhaseTest.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HaplohSeqTest.o src/test/HaplohSeqTest.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HaplohSeqTest.o src/test/HaplohSeqTest.cpp -std=c++14
[*] c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HmmTest.o src/test/HmmTest.cpp
<.> /tmp/biology/haplohseq/work/.gcc/bin/g++ -fstack-protector-strong -D_FORTIFY_SOURCE=2 -Wl,-zrelro -fPIC -O2 -pthread -I/tmp/biology/haplohseq/work/.buildlink/include -I/tmp/biology/haplohseq/work/.buildlink/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HmmTest.o src/test/HmmTest.cpp -std=c++14