[*] cc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include CMakeCCompilerId.c <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include CMakeCCompilerId.c -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -gdwarf-2 [*] cc -print-sysroot <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -print-sysroot -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include [*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include CMakeCXXCompilerId.cpp <.> /home/pbulk/build/joyent/cgatools/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/joyent/cgatools/work/.buildlink/include CMakeCXXCompilerId.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -print-sysroot <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -print-sysroot -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include [*] cc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include -v -o CMakeFiles/cmTC_4c12b.dir/CMakeCCompilerABI.c.o -c /opt/local/share/cmake-3.31/Modules/CMakeCCompilerABI.c <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include -v -o CMakeFiles/cmTC_4c12b.dir/CMakeCCompilerABI.c.o -c /opt/local/share/cmake-3.31/Modules/CMakeCCompilerABI.c -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -gdwarf-2 [*] cc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include -L/opt/local/lib -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -Wl,-R/opt/local/lib -v CMakeFiles/cmTC_4c12b.dir/CMakeCCompilerABI.c.o -o cmTC_4c12b <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include -L/home/pbulk/build/joyent/cgatools/work/.buildlink/lib -pthread -Wl,-rpath,/opt/local/lib -v CMakeFiles/cmTC_4c12b.dir/CMakeCCompilerABI.c.o -o cmTC_4c12b -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -gdwarf-2 -lumem [*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include -v -o CMakeFiles/cmTC_ba851.dir/CMakeCXXCompilerABI.cpp.o -c /opt/local/share/cmake-3.31/Modules/CMakeCXXCompilerABI.cpp <.> /home/pbulk/build/joyent/cgatools/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/joyent/cgatools/work/.buildlink/include -v -o CMakeFiles/cmTC_ba851.dir/CMakeCXXCompilerABI.cpp.o -c /opt/local/share/cmake-3.31/Modules/CMakeCXXCompilerABI.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include -L/opt/local/lib -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -Wl,-R/opt/local/lib -v CMakeFiles/cmTC_ba851.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_ba851 <.> /home/pbulk/build/joyent/cgatools/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/joyent/cgatools/work/.buildlink/include -L/home/pbulk/build/joyent/cgatools/work/.buildlink/lib -pthread -Wl,-rpath,/opt/local/lib -v CMakeFiles/cmTC_ba851.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_ba851 -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -lumem [*] cc -DCMAKE_HAVE_LIBC_PTHREAD -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -o CMakeFiles/cmTC_f2d75.dir/src.c.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/CMakeFiles/CMakeScratch/TryCompile-tRaQud/src.c <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -DCMAKE_HAVE_LIBC_PTHREAD -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -o CMakeFiles/cmTC_f2d75.dir/src.c.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/CMakeFiles/CMakeScratch/TryCompile-tRaQud/src.c -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -gdwarf-2 [*] cc -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -L/opt/local/lib -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -Wl,-R/opt/local/lib CMakeFiles/cmTC_f2d75.dir/src.c.o -o cmTC_f2d75 <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -L/home/pbulk/build/joyent/cgatools/work/.buildlink/lib -pthread -Wl,-rpath,/opt/local/lib CMakeFiles/cmTC_f2d75.dir/src.c.o -o cmTC_f2d75 -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc -gdwarf-2 -lumem [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/CnvSegmentStore.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/CnvSegmentStore.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/CnvDetailStore.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/CnvDetailStore.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/Dnb.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/Dnb.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/EvidenceReader.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/EvidenceReader.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/GenomeMetadata.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/GenomeMetadata.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvSegmentStore.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvSegmentStore.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/LibraryReader.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/LibraryReader.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/ReferenceSupportReader.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/ReferenceSupportReader.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/CallDiff.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/CallDiff.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Command.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Command.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Crr2Fasta.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Crr2Fasta.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/DecodeCrr.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/DecodeCrr.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Evidence2Cache.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Evidence2Cache.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Evidence2Sam.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Evidence2Sam.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Fasta2Crr.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Fasta2Crr.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Join.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Join.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Junction2Vcf.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Junction2Vcf.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/JunctionCmp.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/JunctionCmp.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/GenomeMetadata.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/GenomeMetadata.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/JunctionDiff.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/JunctionDiff.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/JunctionType.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/JunctionType.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/ListCrr.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/ListCrr.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/ListVariants.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/ListVariants.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Map2Sam.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Map2Sam.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/MergedMap2Sam.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/MergedMap2Sam.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/MkVcf.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/MkVcf.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Sam2Reads.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Sam2Reads.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/SnpDiff.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/SnpDiff.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/TestVariants.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/TestVariants.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/VarFileCombine.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/VarFileCombine.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/LibraryReader.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/LibraryReader.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/VarFilter.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/VarFilter.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/conv/VcfRecordSource.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/conv/VcfRecordSource.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/copynumber/CnvFileVcfSource.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/copynumber/CnvFileVcfSource.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/core.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/core.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/Junction.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/Junction.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/ReferenceSupportReader.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/ReferenceSupportReader.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionCompare.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionCompare.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionStat.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionStat.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionVcfRecord.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionVcfRecord.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionVcfWriter.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionVcfWriter.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mainpage.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mainpage.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/AlleleAlignment.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/AlleleAlignment.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/Cigar.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/Cigar.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/EvidenceCache.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/EvidenceCache.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/EvidenceSamUtil.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/EvidenceSamUtil.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/GapsEstimator.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/GapsEstimator.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/LaneBatchCache.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/LaneBatchCache.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/LibraryData.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/LibraryData.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/Map2SamConverter.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/Map2SamConverter.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/MapSamUtils.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/MapSamUtils.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/MergeMap2SamConverter.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/MergeMap2SamConverter.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamOptions.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamOptions.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamReader.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamReader.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamRecord.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamRecord.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/ChromosomeIdField.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/ChromosomeIdField.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CompactDnaSequence.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CompactDnaSequence.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CrrFile.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CrrFile.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Crr2Fasta.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Crr2Fasta.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CrrFileWriter.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CrrFileWriter.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/GeneDataStore.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/GeneDataStore.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/RangeAnnotationStore.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/RangeAnnotationStore.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/RepeatMaskerStore.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/RepeatMaskerStore.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/DecodeCrr.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/DecodeCrr.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/range.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/range.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/BaseUtil.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/BaseUtil.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/DelimitedFile.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/DelimitedFile.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/DelimitedLineParser.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/DelimitedLineParser.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Exception.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Exception.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Files.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Files.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/GenericHistogram.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/GenericHistogram.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Fasta2Crr.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Fasta2Crr.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/IndirectComparator.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/IndirectComparator.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Md5.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Md5.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/RangeIntersector.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/RangeIntersector.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/RangeSet.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/RangeSet.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Streams.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/Streams.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/StringSet.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/StringSet.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/parse.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/parse.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Allele.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Allele.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Junction2Vcf.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Junction2Vcf.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/AlleleDiffSegment.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/AlleleDiffSegment.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Call.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Call.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/CallDiffMatchType.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/CallDiffMatchType.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/CallDiffResult.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/CallDiffResult.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Locus.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Locus.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionCmp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionCmp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionDiff.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionDiff.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/PhasedAllele.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/PhasedAllele.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/PhasedHypothesis.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/PhasedHypothesis.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListCrr.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListCrr.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Superlocus.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Superlocus.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/SuperlocusIterator.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/SuperlocusIterator.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/VariantFileIterator.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/VariantFileIterator.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/VariantFileVcfSource.hpp.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o -MF CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o.d -o CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/VariantFileVcfSource.hpp.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc [*] c++ -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/usr/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Map2Sam.cpp <.> /home/pbulk/build/joyent/cgatools/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -I/home/pbulk/build/joyent/cgatools/work -I/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/. -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/joyent/cgatools/work/.buildlink/include '-DCGA_TOOLS_VERSION="1.8.0"' -DCGA_TOOLS_IS_PIPELINE=0 '-DCGA_TOOLS_BUILD="1"' -DCGA_TOOLS_DEVBUILD=1 -Wall -MD -MT CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o -MF CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o.d -o CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o -c /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Map2Sam.cpp -specs=/home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc