[*] /home/pbulk/build/biology/haplohseq/work/.tools/bin/mkdir -p build build/bin build/obj
<.> /usr/bin/mkdir -p -p build build/bin build/obj
[*] /home/pbulk/build/biology/haplohseq/work/.tools/bin/mkdir -p build/test
<.> /usr/bin/mkdir -p -p build/test
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/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
<.> /home/pbulk/build/biology/haplohseq/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/haplohseq/work/.buildlink/include -I/home/pbulk/build/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