Tried building the Dockerfile exited with error

Tried running docker build hal2vg (git cloned it with --recursive flag) but it came up with this huge error output I have no idea how to troubleshoot:
Sending build context to Docker daemon  15.95MB

Step 1/6 : FROM quay.io/vgteam/vg:v1.11.0-74-gdab42acd-t242-build
 ---> 47dd1bd9832c
Step 2/6 : RUN apt-get -qq update && apt-get -qq install -y libhdf5-serial-dev
 ---> Using cache
 ---> 64e1dae59b51
Step 3/6 : ADD . /hal2vg
 ---> Using cache
 ---> abac8b146f00
Step 4/6 : WORKDIR /hal2vg
 ---> Using cache
 ---> 1722c6427497
Step 5/6 : RUN make
 ---> Running in 1ed54e137a8a
cd deps/sonLib && make
make[1]: Entering directory '/hal2vg/deps/sonLib'
cd externalTools && make all
make[2]: Entering directory '/hal2vg/deps/sonLib/externalTools'
cd cutest && make all
make[3]: Entering directory '/hal2vg/deps/sonLib/externalTools/cutest'
gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG  -c CuTest.c
ar rc cuTest.a *.o
ranlib cuTest.a
rm -f *.o
mv cuTest.a ../../lib/
cp CuTest.h ../../lib/
make[3]: Leaving directory '/hal2vg/deps/sonLib/externalTools/cutest'
cd quicktree_1.1 && make all
make[3]: Entering directory '/hal2vg/deps/sonLib/externalTools/quicktree_1.1'
gcc -c -I./include -O3 -Wall -o ./obj/align.o ./src/align.c
gcc -c -I./include -O3 -Wall -o ./obj/cluster.o ./src/cluster.c
gcc -c -I./include -O3 -Wall -o ./obj/distancemat.o ./src/distancemat.c
[91m./src/distancemat.c: In function 'read_phylip_DistanceMatrix':
[0m[91m./src/distancemat.c:390:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf( handle, "%s", identifier );
     ^
./src/distancemat.c:397:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
       fscanf( handle, "%lf", &dist);
       ^
[0mgcc -c -I./include -O3 -Wall -o ./obj/options.o ./src/options.c
gcc -c -I./include -O3 -Wall -o ./obj/util.o ./src/util.c
gcc -c -I./include -O3 -Wall -o ./obj/sequence.o ./src/sequence.c
gcc -c -I./include -O3 -Wall -o ./obj/quicktree.o ./src/quicktree.c
gcc -c -I./include -O3 -Wall -o ./obj/buildtree.o ./src/buildtree.c
gcc -c -I./include -O3 -Wall -o ./obj/tree.o ./src/tree.c
[91m./src/tree.c: In function 'read_newhampshire_Tnode':
[0m[91m./src/tree.c:393:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf( handle, "%1s", &c);
   ^
./src/tree.c:406:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf( handle, "%1s", &c); /* should be , */
     ^
./src/tree.c:417:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf( handle, "%1s", &c);  /* should be ) */
     ^
./src/tree.c:420:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf( handle, "%1s", &c);  /* should be : */
     ^
[0m[91m./src/tree.c: In function 'read_newhampshire_Tree':
./src/tree.c:468:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf( handle, "(");
   ^
./src/tree.c:475:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf( handle, "%1s", &c ); /* should be , */
   ^
./src/tree.c:484:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf( handle, "%1s", &c ); /* should be , */
   ^
./src/tree.c:493:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf( handle, "%1s", &c);
   ^
./src/tree.c:496:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf( handle, "%1s", &c);
   ^
[0mgcc -g  -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm
make[3]: Leaving directory '/hal2vg/deps/sonLib/externalTools/quicktree_1.1'
make[2]: Leaving directory '/hal2vg/deps/sonLib/externalTools'
cd C && make all
make[2]: Entering directory '/hal2vg/deps/sonLib/C'
cp inc/sonLib.h ../lib/sonLib.h.tmp
mv ../lib/sonLib.h.tmp ../lib/sonLib.h
cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp
mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h
cp inc/stGraph.h ../lib/stGraph.h.tmp
mv ../lib/stGraph.h.tmp ../lib/stGraph.h
cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp
mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h
cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp
mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h
cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp
mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h
cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp
mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h
cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp
mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h
cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp
mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h
cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp
mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h
cp inc/bioioC.h ../lib/bioioC.h.tmp
mv ../lib/bioioC.h.tmp ../lib/bioioC.h
cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp
mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h
cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp
mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h
cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp
mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h
cp inc/commonC.h ../lib/commonC.h.tmp
mv ../lib/commonC.h.tmp ../lib/commonC.h
cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp
mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h
cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp
mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h
cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp
mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h
cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp
mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h
cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp
mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h
cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp
mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h
cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp
mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h
cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp
mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h
cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp
mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h
cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp
mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h
cp inc/avl.h ../lib/avl.h.tmp
mv ../lib/avl.h.tmp ../lib/avl.h
cp inc/sonLibList.h ../lib/sonLibList.h.tmp
mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h
cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp
mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h
cp inc/stMatrix.h ../lib/stMatrix.h.tmp
mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h
cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp
mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h
cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp
mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h
cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp
mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h
cp inc/hashTableC.h ../lib/hashTableC.h.tmp
mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h
cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp
mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h
cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp
mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h
cp inc/stSafeC.h ../lib/stSafeC.h.tmp
mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h
cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp
mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h
cp inc/sonLibString.h ../lib/sonLibString.h.tmp
mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h
gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I inc -I ../lib/  -c impl/*.c
g++ -std=gnu++98 -O3 -g -Wall -funroll-loops -DNDEBUG  -I inc -I ../lib/ -c impl/*.cpp
ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o
ranlib sonLib.a 
rm *.o
mv sonLib.a ../lib/
gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a   -lz -lm  -lm -lstdc++ -lpthread
mv ../bin/sonLibTests.tmp ../bin/sonLibTests
gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a   -lz -lm  -lm
mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest
gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm
mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest
gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm
mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest
make[2]: Leaving directory '/hal2vg/deps/sonLib/C'
cp sonLib_daemonize.py ./bin/sonLib_daemonize.py
chmod +x ./bin/sonLib_daemonize.py
make[1]: Leaving directory '/hal2vg/deps/sonLib'
cd deps/hal && make
make[1]: Entering directory '/hal2vg/deps/hal'
cd api && make libs
make[2]: Entering directory '/hal2vg/deps/hal/api'
h5c++  -MM -MT ../objs/api/impl/halAlignmentInstance.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halAlignmentInstance.cpp >impl/halAlignmentInstance.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halAlignmentInstance.cpp -o ../objs/api/impl/halAlignmentInstance.o
h5c++  -MM -MT ../objs/api/impl/halMappedSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halMappedSegment.cpp >impl/halMappedSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halMappedSegment.cpp -o ../objs/api/impl/halMappedSegment.o
h5c++  -MM -MT ../objs/api/impl/halColumnIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halColumnIterator.cpp >impl/halColumnIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halColumnIterator.cpp -o ../objs/api/impl/halColumnIterator.o
h5c++  -MM -MT ../objs/api/impl/halSegmentIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halSegmentIterator.cpp >impl/halSegmentIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halSegmentIterator.cpp -o ../objs/api/impl/halSegmentIterator.o
h5c++  -MM -MT ../objs/api/impl/halTopSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halTopSegment.cpp >impl/halTopSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halTopSegment.cpp -o ../objs/api/impl/halTopSegment.o
h5c++  -MM -MT ../objs/api/impl/halBottomSegmentIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halBottomSegmentIterator.cpp >impl/halBottomSegmentIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halBottomSegmentIterator.cpp -o ../objs/api/impl/halBottomSegmentIterator.o
h5c++  -MM -MT ../objs/api/impl/halSegmentMapper.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halSegmentMapper.cpp >impl/halSegmentMapper.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halSegmentMapper.cpp -o ../objs/api/impl/halSegmentMapper.o
h5c++  -MM -MT ../objs/api/impl/halValidate.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halValidate.cpp >impl/halValidate.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halValidate.cpp -o ../objs/api/impl/halValidate.o
h5c++  -MM -MT ../objs/api/impl/halGappedBottomSegmentIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halGappedBottomSegmentIterator.cpp >impl/halGappedBottomSegmentIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halGappedBottomSegmentIterator.cpp -o ../objs/api/impl/halGappedBottomSegmentIterator.o
h5c++  -MM -MT ../objs/api/impl/halTopSegmentIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halTopSegmentIterator.cpp >impl/halTopSegmentIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halTopSegmentIterator.cpp -o ../objs/api/impl/halTopSegmentIterator.o
h5c++  -MM -MT ../objs/api/impl/halCLParser.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halCLParser.cpp >impl/halCLParser.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halCLParser.cpp -o ../objs/api/impl/halCLParser.o
h5c++  -MM -MT ../objs/api/impl/halRearrangement.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halRearrangement.cpp >impl/halRearrangement.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halRearrangement.cpp -o ../objs/api/impl/halRearrangement.o
h5c++  -MM -MT ../objs/api/impl/halPositionCache.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halPositionCache.cpp >impl/halPositionCache.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halPositionCache.cpp -o ../objs/api/impl/halPositionCache.o
h5c++  -MM -MT ../objs/api/impl/halCommon.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halCommon.cpp >impl/halCommon.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halCommon.cpp -o ../objs/api/impl/halCommon.o
h5c++  -MM -MT ../objs/api/impl/halSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halSegment.cpp >impl/halSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halSegment.cpp -o ../objs/api/impl/halSegment.o
h5c++  -MM -MT ../objs/api/impl/halBottomSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halBottomSegment.cpp >impl/halBottomSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halBottomSegment.cpp -o ../objs/api/impl/halBottomSegment.o
h5c++  -MM -MT ../objs/api/impl/halGappedTopSegmentIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halGappedTopSegmentIterator.cpp >impl/halGappedTopSegmentIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halGappedTopSegmentIterator.cpp -o ../objs/api/impl/halGappedTopSegmentIterator.o
h5c++  -MM -MT ../objs/api/impl/halGenome.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halGenome.cpp >impl/halGenome.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halGenome.cpp -o ../objs/api/impl/halGenome.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5Sequence.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5Sequence.cpp >hdf5_impl/hdf5Sequence.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5Sequence.cpp -o ../objs/api/hdf5_impl/hdf5Sequence.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5DnaDriver.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5DnaDriver.cpp >hdf5_impl/hdf5DnaDriver.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5DnaDriver.cpp -o ../objs/api/hdf5_impl/hdf5DnaDriver.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5BottomSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5BottomSegment.cpp >hdf5_impl/hdf5BottomSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5BottomSegment.cpp -o ../objs/api/hdf5_impl/hdf5BottomSegment.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5SequenceIterator.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5SequenceIterator.cpp >hdf5_impl/hdf5SequenceIterator.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5SequenceIterator.cpp -o ../objs/api/hdf5_impl/hdf5SequenceIterator.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5Genome.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5Genome.cpp >hdf5_impl/hdf5Genome.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5Genome.cpp -o ../objs/api/hdf5_impl/hdf5Genome.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5TopSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5TopSegment.cpp >hdf5_impl/hdf5TopSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5TopSegment.cpp -o ../objs/api/hdf5_impl/hdf5TopSegment.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5ExternalArray.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5ExternalArray.cpp >hdf5_impl/hdf5ExternalArray.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5ExternalArray.cpp -o ../objs/api/hdf5_impl/hdf5ExternalArray.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5UDCFuseDriver.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5UDCFuseDriver.cpp >hdf5_impl/hdf5UDCFuseDriver.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5UDCFuseDriver.cpp -o ../objs/api/hdf5_impl/hdf5UDCFuseDriver.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5Alignment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5Alignment.cpp >hdf5_impl/hdf5Alignment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5Alignment.cpp -o ../objs/api/hdf5_impl/hdf5Alignment.o
h5c++  -MM -MT ../objs/api/hdf5_impl/hdf5MetaData.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5MetaData.cpp >hdf5_impl/hdf5MetaData.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_impl/hdf5MetaData.cpp -o ../objs/api/hdf5_impl/hdf5MetaData.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapAlignment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapAlignment.cpp >mmap_impl/mmapAlignment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapAlignment.cpp -o ../objs/api/mmap_impl/mmapAlignment.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapGenomeSiteMap.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapGenomeSiteMap.cpp >mmap_impl/mmapGenomeSiteMap.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapGenomeSiteMap.cpp -o ../objs/api/mmap_impl/mmapGenomeSiteMap.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapDnaDriver.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapDnaDriver.cpp >mmap_impl/mmapDnaDriver.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapDnaDriver.cpp -o ../objs/api/mmap_impl/mmapDnaDriver.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapPerfectHashTable.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapPerfectHashTable.cpp >mmap_impl/mmapPerfectHashTable.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapPerfectHashTable.cpp -o ../objs/api/mmap_impl/mmapPerfectHashTable.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapRbTree.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapRbTree.cpp >mmap_impl/mmapRbTree.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapRbTree.cpp -o ../objs/api/mmap_impl/mmapRbTree.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapSequence.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapSequence.cpp >mmap_impl/mmapSequence.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapSequence.cpp -o ../objs/api/mmap_impl/mmapSequence.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapBottomSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapBottomSegment.cpp >mmap_impl/mmapBottomSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapBottomSegment.cpp -o ../objs/api/mmap_impl/mmapBottomSegment.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapFile.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapFile.cpp >mmap_impl/mmapFile.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapFile.cpp -o ../objs/api/mmap_impl/mmapFile.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapGenome.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapGenome.cpp >mmap_impl/mmapGenome.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapGenome.cpp -o ../objs/api/mmap_impl/mmapGenome.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapPhf.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapPhf.cpp >mmap_impl/mmapPhf.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapPhf.cpp -o ../objs/api/mmap_impl/mmapPhf.o
h5c++  -MM -MT ../objs/api/mmap_impl/mmapTopSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapTopSegment.cpp >mmap_impl/mmapTopSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c mmap_impl/mmapTopSegment.cpp -o ../objs/api/mmap_impl/mmapTopSegment.o
ar rc ../lib/libHal.a ../objs/api/impl/halAlignmentInstance.o ../objs/api/impl/halMappedSegment.o ../objs/api/impl/halColumnIterator.o ../objs/api/impl/halSegmentIterator.o ../objs/api/impl/halTopSegment.o ../objs/api/impl/halBottomSegmentIterator.o ../objs/api/impl/halSegmentMapper.o ../objs/api/impl/halValidate.o ../objs/api/impl/halGappedBottomSegmentIterator.o ../objs/api/impl/halTopSegmentIterator.o ../objs/api/impl/halCLParser.o ../objs/api/impl/halRearrangement.o ../objs/api/impl/halPositionCache.o ../objs/api/impl/halCommon.o ../objs/api/impl/halSegment.o ../objs/api/impl/halBottomSegment.o ../objs/api/impl/halGappedTopSegmentIterator.o ../objs/api/impl/halGenome.o ../objs/api/hdf5_impl/hdf5Sequence.o ../objs/api/hdf5_impl/hdf5DnaDriver.o ../objs/api/hdf5_impl/hdf5BottomSegment.o ../objs/api/hdf5_impl/hdf5SequenceIterator.o ../objs/api/hdf5_impl/hdf5Genome.o ../objs/api/hdf5_impl/hdf5TopSegment.o ../objs/api/hdf5_impl/hdf5ExternalArray.o ../objs/api/hdf5_impl/hdf5UDCFuseDriver.o ../objs/api/hdf5_impl/hdf5Alignment.o ../objs/api/hdf5_impl/hdf5MetaData.o ../objs/api/mmap_impl/mmapAlignment.o ../objs/api/mmap_impl/mmapGenomeSiteMap.o ../objs/api/mmap_impl/mmapDnaDriver.o ../objs/api/mmap_impl/mmapPerfectHashTable.o ../objs/api/mmap_impl/mmapRbTree.o ../objs/api/mmap_impl/mmapSequence.o ../objs/api/mmap_impl/mmapBottomSegment.o ../objs/api/mmap_impl/mmapFile.o ../objs/api/mmap_impl/mmapGenome.o ../objs/api/mmap_impl/mmapPhf.o ../objs/api/mmap_impl/mmapTopSegment.o 
ranlib ../lib/libHal.a
h5c++  -MM -MT ../objs/api/tests/halAlignmentTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halAlignmentTest.cpp >tests/halAlignmentTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halAlignmentTest.cpp -o ../objs/api/tests/halAlignmentTest.o
h5c++  -MM -MT ../objs/api/tests/halBottomSegmentTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halBottomSegmentTest.cpp >tests/halBottomSegmentTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halBottomSegmentTest.cpp -o ../objs/api/tests/halBottomSegmentTest.o
h5c++  -MM -MT ../objs/api/tests/halTopSegmentTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halTopSegmentTest.cpp >tests/halTopSegmentTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halTopSegmentTest.cpp -o ../objs/api/tests/halTopSegmentTest.o
h5c++  -MM -MT ../objs/api/tests/halAlignmentInstanceTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halAlignmentInstanceTest.cpp >tests/halAlignmentInstanceTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halAlignmentInstanceTest.cpp -o ../objs/api/tests/halAlignmentInstanceTest.o
h5c++  -MM -MT ../objs/api/tests/halRandomData.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halRandomData.cpp >tests/halRandomData.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halRandomData.cpp -o ../objs/api/tests/halRandomData.o
make[2]: Leaving directory '/hal2vg/deps/hal/api'
cd stats && make libs
make[2]: Entering directory '/hal2vg/deps/hal/stats'
h5c++  -MM -MT ../objs/stats/impl/halStats.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halStats.cpp >impl/halStats.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halStats.cpp -o ../objs/stats/impl/halStats.o
ar rc ../lib/libHalStats.a ../objs/stats/impl/halStats.o
ranlib ../lib/libHalStats.a
make[2]: Leaving directory '/hal2vg/deps/hal/stats'
cd randgen && make libs
make[2]: Entering directory '/hal2vg/deps/hal/randgen'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/randgen'
cd validate && make libs
make[2]: Entering directory '/hal2vg/deps/hal/validate'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/validate'
cd mutations && make libs
make[2]: Entering directory '/hal2vg/deps/hal/mutations'
h5c++  -MM -MT ../objs/mutations/impl/halBranchMutations.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halBranchMutations.cpp >impl/halBranchMutations.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halBranchMutations.cpp -o ../objs/mutations/impl/halBranchMutations.o
h5c++  -MM -MT ../objs/mutations/impl/halMutationsStats.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halMutationsStats.cpp >impl/halMutationsStats.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halMutationsStats.cpp -o ../objs/mutations/impl/halMutationsStats.o
h5c++  -MM -MT ../objs/mutations/impl/halSummarizeMutations.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halSummarizeMutations.cpp >impl/halSummarizeMutations.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halSummarizeMutations.cpp -o ../objs/mutations/impl/halSummarizeMutations.o
ar rc ../lib/libHalMutations.a ../objs/mutations/impl/halBranchMutations.o ../objs/mutations/impl/halMutationsStats.o ../objs/mutations/impl/halSummarizeMutations.o
ranlib ../lib/libHalMutations.a
make[2]: Leaving directory '/hal2vg/deps/hal/mutations'
cd fasta && make libs
make[2]: Entering directory '/hal2vg/deps/hal/fasta'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/fasta'
cd alignmentDepth && make libs
make[2]: Entering directory '/hal2vg/deps/hal/alignmentDepth'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/alignmentDepth'
cd liftover && make libs
make[2]: Entering directory '/hal2vg/deps/hal/liftover'
h5c++  -MM -MT ../objs/liftover/impl/halBedLine.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBedLine.cpp >impl/halBedLine.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBedLine.cpp -o ../objs/liftover/impl/halBedLine.o
h5c++  -MM -MT ../objs/liftover/impl/halBedScanner.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBedScanner.cpp >impl/halBedScanner.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBedScanner.cpp -o ../objs/liftover/impl/halBedScanner.o
h5c++  -MM -MT ../objs/liftover/impl/halBlockLiftover.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBlockLiftover.cpp >impl/halBlockLiftover.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBlockLiftover.cpp -o ../objs/liftover/impl/halBlockLiftover.o
h5c++  -MM -MT ../objs/liftover/impl/halBlockMapper.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBlockMapper.cpp >impl/halBlockMapper.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halBlockMapper.cpp -o ../objs/liftover/impl/halBlockMapper.o
h5c++  -MM -MT ../objs/liftover/impl/halColumnLiftover.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halColumnLiftover.cpp >impl/halColumnLiftover.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halColumnLiftover.cpp -o ../objs/liftover/impl/halColumnLiftover.o
h5c++  -MM -MT ../objs/liftover/impl/halLiftover.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halLiftover.cpp >impl/halLiftover.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halLiftover.cpp -o ../objs/liftover/impl/halLiftover.o
h5c++  -MM -MT ../objs/liftover/impl/halWiggleLiftover.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleLiftover.cpp >impl/halWiggleLiftover.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleLiftover.cpp -o ../objs/liftover/impl/halWiggleLiftover.o
h5c++  -MM -MT ../objs/liftover/impl/halWiggleLoader.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleLoader.cpp >impl/halWiggleLoader.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleLoader.cpp -o ../objs/liftover/impl/halWiggleLoader.o
h5c++  -MM -MT ../objs/liftover/impl/halWiggleScanner.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleScanner.cpp >impl/halWiggleScanner.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleScanner.cpp -o ../objs/liftover/impl/halWiggleScanner.o
ar rc ../lib/libHalLiftover.a ../objs/liftover/impl/halBedLine.o ../objs/liftover/impl/halBedScanner.o ../objs/liftover/impl/halBlockLiftover.o ../objs/liftover/impl/halBlockMapper.o ../objs/liftover/impl/halColumnLiftover.o ../objs/liftover/impl/halLiftover.o ../objs/liftover/impl/halWiggleLiftover.o ../objs/liftover/impl/halWiggleLoader.o ../objs/liftover/impl/halWiggleScanner.o
ranlib ../lib/libHalLiftover.a
make[2]: Leaving directory '/hal2vg/deps/hal/liftover'
cd lod && make libs
make[2]: Entering directory '/hal2vg/deps/hal/lod'
h5c++  -MM -MT ../objs/lod/impl/halLodBlock.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodBlock.cpp >impl/halLodBlock.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodBlock.cpp -o ../objs/lod/impl/halLodBlock.o
h5c++  -MM -MT ../objs/lod/impl/halLodExtract.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodExtract.cpp >impl/halLodExtract.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodExtract.cpp -o ../objs/lod/impl/halLodExtract.o
h5c++  -MM -MT ../objs/lod/impl/halLodGraph.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodGraph.cpp >impl/halLodGraph.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodGraph.cpp -o ../objs/lod/impl/halLodGraph.o
h5c++  -MM -MT ../objs/lod/impl/halLodManager.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodManager.cpp >impl/halLodManager.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodManager.cpp -o ../objs/lod/impl/halLodManager.o
h5c++  -MM -MT ../objs/lod/impl/halLodSegment.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodSegment.cpp >impl/halLodSegment.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodSegment.cpp -o ../objs/lod/impl/halLodSegment.o
ar rc ../lib/libHalLod.a ../objs/lod/impl/halLodBlock.o ../objs/lod/impl/halLodExtract.o ../objs/lod/impl/halLodGraph.o ../objs/lod/impl/halLodManager.o ../objs/lod/impl/halLodSegment.o
ranlib ../lib/libHalLod.a
make[2]: Leaving directory '/hal2vg/deps/hal/lod'
cd maf && make libs
make[2]: Entering directory '/hal2vg/deps/hal/maf'
h5c++  -MM -MT ../objs/maf/impl/halMafBed.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafBed.cpp >impl/halMafBed.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafBed.cpp -o ../objs/maf/impl/halMafBed.o
h5c++  -MM -MT ../objs/maf/impl/halMafBlock.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafBlock.cpp >impl/halMafBlock.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafBlock.cpp -o ../objs/maf/impl/halMafBlock.o
h5c++  -MM -MT ../objs/maf/impl/halMafExport.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafExport.cpp >impl/halMafExport.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafExport.cpp -o ../objs/maf/impl/halMafExport.o
h5c++  -MM -MT ../objs/maf/impl/halMafScanDimensions.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafScanDimensions.cpp >impl/halMafScanDimensions.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafScanDimensions.cpp -o ../objs/maf/impl/halMafScanDimensions.o
h5c++  -MM -MT ../objs/maf/impl/halMafScanner.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafScanner.cpp >impl/halMafScanner.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafScanner.cpp -o ../objs/maf/impl/halMafScanner.o
h5c++  -MM -MT ../objs/maf/impl/halMafScanReference.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafScanReference.cpp >impl/halMafScanReference.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafScanReference.cpp -o ../objs/maf/impl/halMafScanReference.o
h5c++  -MM -MT ../objs/maf/impl/halMafWriteGenomes.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafWriteGenomes.cpp >impl/halMafWriteGenomes.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMafWriteGenomes.cpp -o ../objs/maf/impl/halMafWriteGenomes.o
[91mimpl/halMafWriteGenomes.cpp: In member function 'virtual void hal::MafWriteGenomes::aLine()':
impl/halMafWriteGenomes.cpp:450:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
             system("date");
                           ^
[0mar rc ../lib/libHalMaf.a ../objs/maf/impl/halMafBed.o ../objs/maf/impl/halMafBlock.o ../objs/maf/impl/halMafExport.o ../objs/maf/impl/halMafScanDimensions.o ../objs/maf/impl/halMafScanner.o ../objs/maf/impl/halMafScanReference.o ../objs/maf/impl/halMafWriteGenomes.o
ranlib ../lib/libHalMaf.a
make[2]: Leaving directory '/hal2vg/deps/hal/maf'
cd blockViz && make libs
make[2]: Entering directory '/hal2vg/deps/hal/blockViz'
h5c++  -MM -MT ../objs/blockViz/impl/halBlockViz.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c impl/halBlockViz.cpp >impl/halBlockViz.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c impl/halBlockViz.cpp -o ../objs/blockViz/impl/halBlockViz.o
ar rc ../lib/libHalBlockViz.a ../objs/blockViz/impl/halBlockViz.o
ranlib ../lib/libHalBlockViz.a
make[2]: Leaving directory '/hal2vg/deps/hal/blockViz'
cd extract && make libs
make[2]: Entering directory '/hal2vg/deps/hal/extract'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/extract'
cd analysis && make libs
make[2]: Entering directory '/hal2vg/deps/hal/analysis'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/analysis'
cd phyloP && make libs
make[2]: Entering directory '/hal2vg/deps/hal/phyloP'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/phyloP'
cd modify && make libs
make[2]: Entering directory '/hal2vg/deps/hal/modify'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/modify'
cd assemblyHub && make libs
make[2]: Entering directory '/hal2vg/deps/hal/assemblyHub'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/assemblyHub'
cd synteny && make libs
make[2]: Entering directory '/hal2vg/deps/hal/synteny'
make[2]: Nothing to be done for 'libs'.
make[2]: Leaving directory '/hal2vg/deps/hal/synteny'
cd api && make progs
make[2]: Entering directory '/hal2vg/deps/hal/api'
h5c++  -MM -MT ../objs/api/tests/allTests.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/allTests.cpp >tests/allTests.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/allTests.cpp -o ../objs/api/tests/allTests.o
h5c++  -MM -MT ../objs/api/tests/halMappedSegmentTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halMappedSegmentTest.cpp >tests/halMappedSegmentTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halMappedSegmentTest.cpp -o ../objs/api/tests/halMappedSegmentTest.o
h5c++  -MM -MT ../objs/api/tests/halSequenceTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halSequenceTest.cpp >tests/halSequenceTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halSequenceTest.cpp -o ../objs/api/tests/halSequenceTest.o
h5c++  -MM -MT ../objs/api/tests/halColumnIteratorTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halColumnIteratorTest.cpp >tests/halColumnIteratorTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halColumnIteratorTest.cpp -o ../objs/api/tests/halColumnIteratorTest.o
h5c++  -MM -MT ../objs/api/tests/halGenomeTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halGenomeTest.cpp >tests/halGenomeTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halGenomeTest.cpp -o ../objs/api/tests/halGenomeTest.o
h5c++  -MM -MT ../objs/api/tests/halGappedSegmentIteratorTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halGappedSegmentIteratorTest.cpp >tests/halGappedSegmentIteratorTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halGappedSegmentIteratorTest.cpp -o ../objs/api/tests/halGappedSegmentIteratorTest.o
h5c++  -MM -MT ../objs/api/tests/halRearrangementTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halRearrangementTest.cpp >tests/halRearrangementTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halRearrangementTest.cpp -o ../objs/api/tests/halRearrangementTest.o
h5c++  -MM -MT ../objs/api/tests/halMetaDataTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halMetaDataTest.cpp >tests/halMetaDataTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halMetaDataTest.cpp -o ../objs/api/tests/halMetaDataTest.o
h5c++  -MM -MT ../objs/api/tests/halValidateTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halValidateTest.cpp >tests/halValidateTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c tests/halValidateTest.cpp -o ../objs/api/tests/halValidateTest.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -I tests -o ../bin/halApiTests ../objs/api/tests/allTests.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halMappedSegmentTest.o ../objs/api/tests/halSequenceTest.o ../objs/api/tests/halColumnIteratorTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halGenomeTest.o ../objs/api/tests/halRandomData.o ../objs/api/tests/halGappedSegmentIteratorTest.o ../objs/api/tests/halRearrangementTest.o ../objs/api/tests/halMetaDataTest.o ../objs/api/tests/halValidateTest.o ../objs/api/tests/halBottomSegmentTest.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/api/hdf5_tests/hdf5SegmentTypeTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5SegmentTypeTest.cpp >hdf5_tests/hdf5SegmentTypeTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5SegmentTypeTest.cpp -o ../objs/api/hdf5_tests/hdf5SegmentTypeTest.o
h5c++  -MM -MT ../objs/api/hdf5_tests/hdf5DnaTypeTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5DnaTypeTest.cpp >hdf5_tests/hdf5DnaTypeTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5DnaTypeTest.cpp -o ../objs/api/hdf5_tests/hdf5DnaTypeTest.o
h5c++  -MM -MT ../objs/api/hdf5_tests/hdf5ExternalArrayTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5ExternalArrayTest.cpp >hdf5_tests/hdf5ExternalArrayTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5ExternalArrayTest.cpp -o ../objs/api/hdf5_tests/hdf5ExternalArrayTest.o
h5c++  -MM -MT ../objs/api/hdf5_tests/allTests.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/allTests.cpp >hdf5_tests/allTests.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/allTests.cpp -o ../objs/api/hdf5_tests/allTests.o
h5c++  -MM -MT ../objs/api/hdf5_tests/hdf5SequenceTypeTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5SequenceTypeTest.cpp >hdf5_tests/hdf5SequenceTypeTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5SequenceTypeTest.cpp -o ../objs/api/hdf5_tests/hdf5SequenceTypeTest.o
h5c++  -MM -MT ../objs/api/hdf5_tests/hdf5Test.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5Test.cpp >hdf5_tests/hdf5Test.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c hdf5_tests/hdf5Test.cpp -o ../objs/api/hdf5_tests/hdf5Test.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -I tests -o ../bin/halHdf5Tests ../objs/api/hdf5_tests/hdf5SegmentTypeTest.o ../objs/api/hdf5_tests/hdf5DnaTypeTest.o ../objs/api/hdf5_tests/hdf5ExternalArrayTest.o ../objs/api/hdf5_tests/allTests.o ../objs/api/hdf5_tests/hdf5SequenceTypeTest.o ../objs/api/hdf5_tests/hdf5Test.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/api'
cd stats && make progs
make[2]: Entering directory '/hal2vg/deps/hal/stats'
h5c++  -MM -MT ../objs/stats/impl/halStatsMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halStatsMain.cpp >impl/halStatsMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halStatsMain.cpp -o ../objs/stats/impl/halStatsMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halStats ../objs/stats/impl/halStatsMain.o ../lib/libHalStats.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/stats/impl/halCoverage.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halCoverage.cpp >impl/halCoverage.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halCoverage.cpp -o ../objs/stats/impl/halCoverage.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halCoverage ../objs/stats/impl/halCoverage.o ../lib/libHalStats.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/stats/impl/halPctIdentity.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halPctIdentity.cpp >impl/halPctIdentity.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halPctIdentity.cpp -o ../objs/stats/impl/halPctIdentity.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halPctId ../objs/stats/impl/halPctIdentity.o ../lib/libHalStats.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/stats'
cd randgen && make progs
make[2]: Entering directory '/hal2vg/deps/hal/randgen'
h5c++  -MM -MT ../objs/randgen/halRandGen.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c halRandGen.cpp >halRandGen.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c halRandGen.cpp -o ../objs/randgen/halRandGen.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -I tests -o ../bin/halRandGen ../objs/randgen/halRandGen.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/randgen/halTestGen.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c halTestGen.cpp >halTestGen.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c halTestGen.cpp -o ../objs/randgen/halTestGen.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -I tests -o ../bin/halTestGen ../objs/randgen/halTestGen.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/randgen'
cd validate && make progs
make[2]: Entering directory '/hal2vg/deps/hal/validate'
h5c++  -MM -MT ../objs/validate/halValidateMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../stats/inc/ -c halValidateMain.cpp >halValidateMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../stats/inc/ -c halValidateMain.cpp -o ../objs/validate/halValidateMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../stats/inc/ -I tests -o ../bin/halValidate ../objs/validate/halValidateMain.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/validate'
cd mutations && make progs
make[2]: Entering directory '/hal2vg/deps/hal/mutations'
h5c++  -MM -MT ../objs/mutations/impl/halIndels.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halIndels.cpp >impl/halIndels.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halIndels.cpp -o ../objs/mutations/impl/halIndels.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halIndels ../objs/mutations/impl/halIndels.o ../lib/libHalMutations.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/mutations/impl/halBranchMutationsMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halBranchMutationsMain.cpp >impl/halBranchMutationsMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halBranchMutationsMain.cpp -o ../objs/mutations/impl/halBranchMutationsMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halBranchMutations ../objs/mutations/impl/halBranchMutationsMain.o ../lib/libHalMutations.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/mutations/impl/halSnps.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halSnps.cpp >impl/halSnps.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halSnps.cpp -o ../objs/mutations/impl/halSnps.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halSnps ../objs/mutations/impl/halSnps.o ../lib/libHalMutations.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/mutations/impl/halSummarizeMutationsMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halSummarizeMutationsMain.cpp >impl/halSummarizeMutationsMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halSummarizeMutationsMain.cpp -o ../objs/mutations/impl/halSummarizeMutationsMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halSummarizeMutations ../objs/mutations/impl/halSummarizeMutationsMain.o ../lib/libHalMutations.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/mutations'
cd fasta && make progs
make[2]: Entering directory '/hal2vg/deps/hal/fasta'
h5c++  -MM -MT ../objs/fasta/hal2fasta.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c hal2fasta.cpp >hal2fasta.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c hal2fasta.cpp -o ../objs/fasta/hal2fasta.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/hal2fasta ../objs/fasta/hal2fasta.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/fasta'
cd alignmentDepth && make progs
make[2]: Entering directory '/hal2vg/deps/hal/alignmentDepth'
h5c++  -MM -MT ../objs/alignmentDepth/halAlignmentDepth.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c halAlignmentDepth.cpp >halAlignmentDepth.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c halAlignmentDepth.cpp -o ../objs/alignmentDepth/halAlignmentDepth.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halAlignmentDepth ../objs/alignmentDepth/halAlignmentDepth.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/alignmentDepth'
cd liftover && make progs
make[2]: Entering directory '/hal2vg/deps/hal/liftover'
h5c++  -MM -MT ../objs/liftover/impl/halLiftoverMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halLiftoverMain.cpp >impl/halLiftoverMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halLiftoverMain.cpp -o ../objs/liftover/impl/halLiftoverMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -I tests -o ../bin/halLiftover ../objs/liftover/impl/halLiftoverMain.o ../lib/libHalLiftover.a ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/liftover/impl/halWiggleLiftoverMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleLiftoverMain.cpp >impl/halWiggleLiftoverMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c impl/halWiggleLiftoverMain.cpp -o ../objs/liftover/impl/halWiggleLiftoverMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -I tests -o ../bin/halWiggleLiftover ../objs/liftover/impl/halWiggleLiftoverMain.o ../lib/libHalLiftover.a ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/liftover/tests/halLiftoverTests.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c tests/halLiftoverTests.cpp >tests/halLiftoverTests.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -c tests/halLiftoverTests.cpp -o ../objs/liftover/tests/halLiftoverTests.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../api/tests -I tests -o ../bin/halLiftoverTests ../objs/liftover/tests/halLiftoverTests.o ../lib/libHalLiftover.a ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/liftover'
cd lod && make progs
make[2]: Entering directory '/hal2vg/deps/hal/lod'
h5c++  -MM -MT ../objs/lod/impl/halLodExtractMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodExtractMain.cpp >impl/halLodExtractMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -c impl/halLodExtractMain.cpp -o ../objs/lod/impl/halLodExtractMain.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I tests -o ../bin/halLodExtract ../objs/lod/impl/halLodExtractMain.o ../lib/libHalLod.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/lod'
cd maf && make progs
make[2]: Entering directory '/hal2vg/deps/hal/maf'
h5c++  -MM -MT ../objs/maf/impl/hal2maf.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/hal2maf.cpp >impl/hal2maf.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/hal2maf.cpp -o ../objs/maf/impl/hal2maf.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/hal2maf ../objs/maf/impl/hal2maf.o ../lib/libHalMaf.a ../lib/libHalLiftover.a ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/maf/impl/maf2hal.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/maf2hal.cpp >impl/maf2hal.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/maf2hal.cpp -o ../objs/maf/impl/maf2hal.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/maf2hal ../objs/maf/impl/maf2hal.o ../lib/libHalMaf.a ../lib/libHalLiftover.a ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/maf/tests/halMafTests.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/halMafTests.cpp >tests/halMafTests.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/halMafTests.cpp -o ../objs/maf/tests/halMafTests.o
h5c++  -MM -MT ../objs/maf/tests/halMafBlockTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/halMafBlockTest.cpp >tests/halMafBlockTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/halMafBlockTest.cpp -o ../objs/maf/tests/halMafBlockTest.o
h5c++  -MM -MT ../objs/maf/tests/halMafExportTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/halMafExportTest.cpp >tests/halMafExportTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/halMafExportTest.cpp -o ../objs/maf/tests/halMafExportTest.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/halMafTests ../objs/maf/tests/halMafTests.o ../objs/maf/tests/halMafBlockTest.o ../objs/maf/tests/halMafExportTest.o ../lib/libHalMaf.a ../lib/libHalLiftover.a ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
cp -f hal2mafMP.py ../bin/hal2mafMP.py
chmod u+x,a-w ../bin/hal2mafMP.py
make[2]: Leaving directory '/hal2vg/deps/hal/maf'
cd blockViz && make progs
make[2]: Entering directory '/hal2vg/deps/hal/blockViz'
h5c++  -MM -MT ../objs/blockViz/tests/blockVizBed.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c tests/blockVizBed.cpp >tests/blockVizBed.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c tests/blockVizBed.cpp -o ../objs/blockViz/tests/blockVizBed.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -I tests -o ../bin/blockVizBed ../objs/blockViz/tests/blockVizBed.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalBlockViz.a ../lib/libHalLiftover.a ../lib/libHalLod.a ../lib/libHalMaf.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/blockViz/tests/blockVizMaf.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c tests/blockVizMaf.cpp >tests/blockVizMaf.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c tests/blockVizMaf.cpp -o ../objs/blockViz/tests/blockVizMaf.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -I tests -o ../bin/blockVizMaf ../objs/blockViz/tests/blockVizMaf.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalBlockViz.a ../lib/libHalLiftover.a ../lib/libHalLod.a ../lib/libHalMaf.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/blockViz/tests/blockVizTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c tests/blockVizTest.cpp >tests/blockVizTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -c tests/blockVizTest.cpp -o ../objs/blockViz/tests/blockVizTest.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../lod/inc -I../maf/inc -I../api/tests -I tests -o ../bin/blockVizTest ../objs/blockViz/tests/blockVizTest.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalBlockViz.a ../lib/libHalLiftover.a ../lib/libHalLod.a ../lib/libHalMaf.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/blockViz'
cd extract && make progs
make[2]: Entering directory '/hal2vg/deps/hal/extract'
h5c++  -MM -MT ../objs/extract/impl/halExtract.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halExtract.cpp >impl/halExtract.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halExtract.cpp -o ../objs/extract/impl/halExtract.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/halExtract ../objs/extract/impl/halExtract.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/extract/impl/halAlignedExtract.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halAlignedExtract.cpp >impl/halAlignedExtract.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halAlignedExtract.cpp -o ../objs/extract/impl/halAlignedExtract.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/halAlignedExtract ../objs/extract/impl/halAlignedExtract.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/extract/impl/halMaskExtractMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMaskExtractMain.cpp >impl/halMaskExtractMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMaskExtractMain.cpp -o ../objs/extract/impl/halMaskExtractMain.o
h5c++  -MM -MT ../objs/extract/impl/halMaskExtractor.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMaskExtractor.cpp >impl/halMaskExtractor.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halMaskExtractor.cpp -o ../objs/extract/impl/halMaskExtractor.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/halMaskExtract ../objs/extract/impl/halMaskExtractMain.o ../objs/extract/impl/halMaskExtractor.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/extract/impl/hal4dExtractMain.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/hal4dExtractMain.cpp >impl/hal4dExtractMain.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/hal4dExtractMain.cpp -o ../objs/extract/impl/hal4dExtractMain.o
h5c++  -MM -MT ../objs/extract/impl/hal4dExtract.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/hal4dExtract.cpp >impl/hal4dExtract.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/hal4dExtract.cpp -o ../objs/extract/impl/hal4dExtract.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/hal4dExtract ../objs/extract/impl/hal4dExtractMain.o ../objs/extract/impl/hal4dExtract.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/extract/impl/halSingleCopyRegionsExtract.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halSingleCopyRegionsExtract.cpp >impl/halSingleCopyRegionsExtract.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c impl/halSingleCopyRegionsExtract.cpp -o ../objs/extract/impl/halSingleCopyRegionsExtract.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/halSingleCopyRegionsExtract ../objs/extract/impl/halSingleCopyRegionsExtract.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/extract/tests/hal4dExtractTest.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/hal4dExtractTest.cpp >tests/hal4dExtractTest.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -c tests/hal4dExtractTest.cpp -o ../objs/extract/tests/hal4dExtractTest.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I../api/tests -I tests -o ../bin/hal4dExtractTest ../objs/extract/tests/hal4dExtractTest.o ../objs/extract/impl/hal4dExtract.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halRandomData.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/extract'
cd analysis && make progs
make[2]: Entering directory '/hal2vg/deps/hal/analysis'
cp -f neutralIndel/halTreeNIConservation.py ../bin/halTreeNIConservation.py
chmod u+x,a-w ../bin/halTreeNIConservation.py
cp -f neutralIndel/halTreeNIBackground.py ../bin/halTreeNIBackground.py
chmod u+x,a-w ../bin/halTreeNIBackground.py
cp -f neutralIndel/halTreeNITurnover.py ../bin/halTreeNITurnover.py
chmod u+x,a-w ../bin/halTreeNITurnover.py
make[2]: Leaving directory '/hal2vg/deps/hal/analysis'
cd phyloP && make progs
make[2]: Entering directory '/hal2vg/deps/hal/phyloP'
make[2]: Nothing to be done for 'progs'.
make[2]: Leaving directory '/hal2vg/deps/hal/phyloP'
cd modify && make progs
make[2]: Entering directory '/hal2vg/deps/hal/modify'
h5c++  -MM -MT ../objs/modify/halRemoveGenome.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halRemoveGenome.cpp >halRemoveGenome.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halRemoveGenome.cpp -o ../objs/modify/halRemoveGenome.o
h5c++  -MM -MT ../objs/modify/markAncestors.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c markAncestors.cpp >markAncestors.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c markAncestors.cpp -o ../objs/modify/markAncestors.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halRemoveGenome ../objs/modify/halRemoveGenome.o ../objs/modify/markAncestors.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halAddToBranch.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halAddToBranch.cpp >halAddToBranch.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halAddToBranch.cpp -o ../objs/modify/halAddToBranch.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halAddToBranch ../objs/modify/halAddToBranch.o ../objs/modify/markAncestors.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halReplaceGenome.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halReplaceGenome.cpp >halReplaceGenome.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halReplaceGenome.cpp -o ../objs/modify/halReplaceGenome.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halReplaceGenome ../objs/modify/halReplaceGenome.o ../objs/modify/markAncestors.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halAppendSubtree.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halAppendSubtree.cpp >halAppendSubtree.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halAppendSubtree.cpp -o ../objs/modify/halAppendSubtree.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halAppendSubtree ../objs/modify/halAppendSubtree.o ../objs/modify/markAncestors.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/findRegionsExclusivelyInGroup.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c findRegionsExclusivelyInGroup.cpp >findRegionsExclusivelyInGroup.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c findRegionsExclusivelyInGroup.cpp -o ../objs/modify/findRegionsExclusivelyInGroup.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/findRegionsExclusivelyInGroup ../objs/modify/findRegionsExclusivelyInGroup.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halUpdateBranchLengths.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halUpdateBranchLengths.cpp >halUpdateBranchLengths.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halUpdateBranchLengths.cpp -o ../objs/modify/halUpdateBranchLengths.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halUpdateBranchLengths ../objs/modify/halUpdateBranchLengths.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halWriteNucleotides.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halWriteNucleotides.cpp >halWriteNucleotides.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halWriteNucleotides.cpp -o ../objs/modify/halWriteNucleotides.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halWriteNucleotides ../objs/modify/halWriteNucleotides.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halSetMetadata.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halSetMetadata.cpp >halSetMetadata.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halSetMetadata.cpp -o ../objs/modify/halSetMetadata.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halSetMetadata ../objs/modify/halSetMetadata.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halRenameGenomes.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halRenameGenomes.cpp >halRenameGenomes.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halRenameGenomes.cpp -o ../objs/modify/halRenameGenomes.o
h5c++  -MM -MT ../objs/modify/renameFile.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c renameFile.cpp >renameFile.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c renameFile.cpp -o ../objs/modify/renameFile.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halRenameGenomes ../objs/modify/halRenameGenomes.o ../objs/modify/renameFile.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
h5c++  -MM -MT ../objs/modify/halRenameSequences.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halRenameSequences.cpp >halRenameSequences.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c halRenameSequences.cpp -o ../objs/modify/halRenameSequences.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halRenameSequences ../objs/modify/halRenameSequences.o ../objs/modify/renameFile.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/modify'
cd assemblyHub && make progs
make[2]: Entering directory '/hal2vg/deps/hal/assemblyHub'
cp -f hal2assemblyHub.py ../bin/hal2assemblyHub.py
chmod u+x,a-w ../bin/hal2assemblyHub.py
make[2]: Leaving directory '/hal2vg/deps/hal/assemblyHub'
cd synteny && make progs
make[2]: Entering directory '/hal2vg/deps/hal/synteny'
h5c++  -MM -MT ../objs/synteny/impl/main.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/main.cpp >impl/main.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/main.cpp -o ../objs/synteny/impl/main.o
h5c++  -MM -MT ../objs/synteny/impl/hal2psl.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/hal2psl.cpp >impl/hal2psl.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/hal2psl.cpp -o ../objs/synteny/impl/hal2psl.o
h5c++  -MM -MT ../objs/synteny/impl/psl_io.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/psl_io.cpp >impl/psl_io.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/psl_io.cpp -o ../objs/synteny/impl/psl_io.o
h5c++  -MM -MT ../objs/synteny/impl/psl_merger.o -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/psl_merger.cpp >impl/psl_merger.depend
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/psl_merger.cpp -o ../objs/synteny/impl/psl_merger.o
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/hal2synteny ../objs/synteny/impl/main.o ../objs/synteny/impl/hal2psl.o ../objs/synteny/impl/psl_io.o ../objs/synteny/impl/psl_merger.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
make[2]: Leaving directory '/hal2vg/deps/hal/synteny'
make[1]: Leaving directory '/hal2vg/deps/hal'
cd deps/hal2sg && make
make[1]: Entering directory '/hal2vg/deps/hal2sg'
cd .//sgExport && make
make[2]: Entering directory '/hal2vg/deps/hal2sg/sgExport'
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I ../../sonLib/lib  -I ../../hal/api/inc -I ../../hal/liftover/inc -I ../sgExport -UNDEBUG -I . sidegraph.cpp -c
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I ../../sonLib/lib  -I ../../hal/api/inc -I ../../hal/liftover/inc -I ../sgExport -UNDEBUG -I . sglookup.cpp -c
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I ../../sonLib/lib  -I ../../hal/api/inc -I ../../hal/liftover/inc -I ../sgExport -UNDEBUG -I . md5.cpp -c
[91mmd5.cpp: In static member function 'static MD5::uint4 MD5::F(MD5::uint4, MD5::uint4, MD5::uint4)':
md5.cpp:65:11: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
   return x&y | ~x&z;
           ^
[0m[91mmd5.cpp: In static member function 'static MD5::uint4 MD5::G(MD5::uint4, MD5::uint4, MD5::uint4)':
md5.cpp:69:11: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
   return x&z | y&~z;
           ^
[0mh5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I ../../sonLib/lib  -I ../../hal/api/inc -I ../../hal/liftover/inc -I ../sgExport -UNDEBUG -I . sgsql.cpp -c
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I ../../sonLib/lib  -I ../../hal/api/inc -I ../../hal/liftover/inc -I ../sgExport -UNDEBUG -I. side2seq.cpp -c
[91mside2seq.cpp: In member function 'void Side2Seq::init(const SideGraph*, const std::vector<std::__cxx11::basic_string<char> >*, const std::vector<std::pair<std::__cxx11::basic_string<char>, std::vector<SGSegment> > >*, bool, bool, const string&, int, bool)':
side2seq.cpp:76:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < _inPaths->size(); ++i)
                     ^
[0m[91mside2seq.cpp: In member function 'void Side2Seq::convert()':
side2seq.cpp:108:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < _inPaths->size(); ++i)
                     ^
[0m[91mIn file included from /usr/include/c++/5/cassert:43:0,
                 from sgcommon.h:11,
                 from sgsequence.h:11,
                 from sgposition.h:11,
                 from sgside.h:10,
                 from sgjoin.h:10,
                 from sidegraph.h:24,
                 from side2seq.h:20,
                 from side2seq.cpp:11:
side2seq.cpp: In member function 'void Side2Seq::addOutSequence(const SGSequence*, const SGPosition&, const SGPosition&)':
side2seq.cpp:190:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   assert(_outBases.size() == outSeq->getID());
                           ^
[0m[91mside2seq.cpp: In member function 'void Side2Seq::convertPath(const SGNamedPath&)':
side2seq.cpp:238:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < inPath.second.size(); ++i)
                     ^
[0m[91mside2seq.cpp:251:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int j = 0; j < frag.size(); ++j)
                       ^
[0mar rc sgExport.a sidegraph.o sglookup.o md5.o sgsql.o side2seq.o
make[2]: Leaving directory '/hal2vg/deps/hal2sg/sgExport'
h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I .//../sonLib/lib  -I .//../hal/api/inc -I .//../hal/liftover/inc -I .//sgExport -UNDEBUG -I . hal2sg.cpp -c
[91mIn file included from .//../hal/api/inc/halAlignment.h:11:0,
                 from .//../hal/api/inc/hal.h:62,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:84:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Alignment)
     ^
.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:84:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Alignment)
     ^
.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:85:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Genome)
     ^
.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:85:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Genome)
     ^
.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:86:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(MetaData)
     ^
[0m[91m.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:86:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(MetaData)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:87:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(TopSegment)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:88:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(BottomSegment)
     ^
.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:89:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Segment)
     ^
.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:89:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Segment)
     ^
.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:90:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Sequence)
     ^
.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:90:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Sequence)
     ^
.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:91:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(SlicedSegment)
     ^
.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:91:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(SlicedSegment)
     ^
[0m[91m.//../hal/api/inc/halDefs.h:77:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;                                                                                         \
                  ^
.//../hal/api/inc/halDefs.h:92:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Rearrangement)
     ^
.//../hal/api/inc/halDefs.h:78:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<const T> T##ConstPtr;
                  ^
.//../hal/api/inc/halDefs.h:92:5: note: in expansion of macro 'HAL_FORWARD_DEC_CLASS'
     HAL_FORWARD_DEC_CLASS(Rearrangement)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:93:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(DnaAccess)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:94:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(MappedSegment)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:95:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(SegmentIterator)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:96:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(GappedSegmentIterator)
     ^
[0m[91m.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:97:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(TopSegmentIterator)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:98:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(GappedTopSegmentIterator)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:99:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(BottomSegmentIterator)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:100:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(GappedBottomSegmentIterator)
     ^
[0m[91m.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:101:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(DnaIterator)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:102:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(SequenceIterator)
     ^
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halDefs.h:103:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(ColumnIterator)
     ^
[0m[91mIn file included from .//../hal/api/inc/halSegment.h:12:0,
                 from .//../hal/api/inc/halBottomSegment.h:12,
                 from .//../hal/api/inc/hal.h:64,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halMappedSegmentContainers.h:20:36: error: 'MappedSegmentPtr' in namespace 'hal' does not name a type
         bool operator()(const hal::MappedSegmentPtr &m1, const hal::MappedSegmentPtr &m2) const;
                                    ^
.//../hal/api/inc/halMappedSegmentContainers.h:20:69: error: 'MappedSegmentPtr' in namespace 'hal' does not name a type
         bool operator()(const hal::MappedSegmentPtr &m1, const hal::MappedSegmentPtr &m2) const;
                                                                     ^
[0m[91m.//../hal/api/inc/halMappedSegmentContainers.h:24:46: error: 'MappedSegmentPtr' was not declared in this scope
     class MappedSegmentSet : public std::set<MappedSegmentPtr, MappedSegmentLess> {};
                                              ^
.//../hal/api/inc/halMappedSegmentContainers.h:24:81: error: template argument 1 is invalid
     class MappedSegmentSet : public std::set<MappedSegmentPtr, MappedSegmentLess> {};
                                                                                 ^
.//../hal/api/inc/halMappedSegmentContainers.h:24:81: error: template argument 3 is invalid
[0m[91mIn file included from .//../hal/api/inc/halGenome.h:13:0,
                 from .//../hal/api/inc/halBottomSegmentIterator.h:13,
                 from .//../hal/api/inc/hal.h:65,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halSegmentedSequence.h:42:17: error: 'TopSegmentIteratorPtr' does not name a type
         virtual TopSegmentIteratorPtr getTopSegmentIterator(hal_index_t position = 0) = 0;
                 ^
.//../hal/api/inc/halSegmentedSequence.h:46:17: error: 'TopSegmentIteratorPtr' does not name a type
         virtual TopSegmentIteratorPtr getTopSegmentIterator(hal_index_t position = 0) const = 0;
                 ^
.//../hal/api/inc/halSegmentedSequence.h:50:17: error: 'BottomSegmentIteratorPtr' does not name a type
         virtual BottomSegmentIteratorPtr getBottomSegmentIterator(hal_index_t position = 0) = 0;
                 ^
.//../hal/api/inc/halSegmentedSequence.h:54:17: error: 'BottomSegmentIteratorPtr' does not name a type
         virtual BottomSegmentIteratorPtr getBottomSegmentIterator(hal_index_t position = 0) const = 0;
                 ^
.//../hal/api/inc/halSegmentedSequence.h:58:17: error: 'DnaIteratorPtr' does not name a type
         virtual DnaIteratorPtr getDnaIterator(hal_index_t position = 0) = 0;
                 ^
[0m[91m.//../hal/api/inc/halSegmentedSequence.h:62:17: error: 'DnaIteratorPtr' does not name a type
         virtual DnaIteratorPtr getDnaIterator(hal_index_t position = 0) const = 0;
                 ^
.//../hal/api/inc/halSegmentedSequence.h:83:17: error: 'ColumnIteratorPtr' does not name a type
         virtual ColumnIteratorPtr getColumnIterator(const std::set<const Genome *> *targets = NULL,
                 ^
.//../hal/api/inc/halSegmentedSequence.h:120:17: error: 'RearrangementPtr' does not name a type
         virtual RearrangementPtr getRearrangement(hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold,
                 ^
[0m[91m.//../hal/api/inc/halSegmentedSequence.h:128:17: error: 'GappedTopSegmentIteratorPtr' does not name a type
         virtual GappedTopSegmentIteratorPtr getGappedTopSegmentIterator(hal_index_t i, hal_size_t gapThreshold,
                 ^
.//../hal/api/inc/halSegmentedSequence.h:136:17: error: 'GappedBottomSegmentIteratorPtr' does not name a type
         virtual GappedBottomSegmentIteratorPtr getGappedBottomSegmentIterator(hal_index_t i, hal_size_t childIdx,
                 ^
[0m[91mIn file included from .//../hal/api/inc/halGenome.h:14:0,
                 from .//../hal/api/inc/halBottomSegmentIterator.h:13,
                 from .//../hal/api/inc/hal.h:65,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halSequence.h:100:17: error: 'TopSegmentIteratorPtr' does not name a type
         virtual TopSegmentIteratorPtr getTopSegmentIterator(hal_index_t position = 0) = 0;
                 ^
.//../hal/api/inc/halSequence.h:104:17: error: 'TopSegmentIteratorPtr' does not name a type
         virtual TopSegmentIteratorPtr getTopSegmentIterator(hal_index_t position = 0) const = 0;
                 ^
.//../hal/api/inc/halSequence.h:108:17: error: 'BottomSegmentIteratorPtr' does not name a type
         virtual BottomSegmentIteratorPtr getBottomSegmentIterator(hal_index_t position = 0) = 0;
                 ^
.//../hal/api/inc/halSequence.h:112:17: error: 'BottomSegmentIteratorPtr' does not name a type
         virtual BottomSegmentIteratorPtr getBottomSegmentIterator(hal_index_t position = 0) const = 0;
                 ^
.//../hal/api/inc/halSequence.h:116:17: error: 'DnaIteratorPtr' does not name a type
         virtual DnaIteratorPtr getDnaIterator(hal_index_t position = 0) = 0;
                 ^
[0m[91m.//../hal/api/inc/halSequence.h:120:17: error: 'DnaIteratorPtr' does not name a type
         virtual DnaIteratorPtr getDnaIterator(hal_index_t position = 0) const = 0;
                 ^
.//../hal/api/inc/halSequence.h:141:17: error: 'ColumnIteratorPtr' does not name a type
         virtual ColumnIteratorPtr getColumnIterator(const std::set<const Genome *> *targets = NULL,
                 ^
[0m[91mIn file included from .//../hal/api/inc/halBottomSegmentIterator.h:13:0,
                 from .//../hal/api/inc/hal.h:65,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halGenome.h:83:17: error: 'SequenceIteratorPtr' does not name a type
         virtual SequenceIteratorPtr getSequenceIterator(hal_index_t position = 0) = 0;
                 ^
.//../hal/api/inc/halGenome.h:87:17: error: 'SequenceIteratorPtr' does not name a type
         virtual SequenceIteratorPtr getSequenceIterator(hal_index_t position = 0) const = 0;
                 ^
[0m[91mIn file included from .//../hal/api/inc/halAlignment.h:11:0,
                 from .//../hal/api/inc/hal.h:62,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halDefs.h:82:18: error: 'shared_ptr' in namespace 'std' does not name a template type
     typedef std::shared_ptr<T> T##Ptr;
                  ^
.//../hal/api/inc/halSegmentIterator.h:120:5: note: in expansion of macro 'HAL_FORWARD_DEC_MUTABLE_CLASS'
     HAL_FORWARD_DEC_MUTABLE_CLASS(SegmentIterator)
     ^
[0m[91mIn file included from .//../hal/api/inc/halBottomSegmentIterator.h:14:0,
                 from .//../hal/api/inc/hal.h:65,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halSegmentIterator.h:126:27: error: declaration of 'operator<' as non-function
     inline bool operator<(SegmentIteratorPtr segmentIt, hal_index_t genomePos) {
                           ^
.//../hal/api/inc/halSegmentIterator.h:126:27: error: 'SegmentIteratorPtr' was not declared in this scope
.//../hal/api/inc/halSegmentIterator.h:126:69: error: expected primary-expression before 'genomePos'
     inline bool operator<(SegmentIteratorPtr segmentIt, hal_index_t genomePos) {
                                                                     ^
[0m[91m.//../hal/api/inc/halSegmentIterator.h:130:27: error: declaration of 'operator>' as non-function
     inline bool operator>(SegmentIteratorPtr segmentIt, hal_index_t genomePos) {
                           ^
.//../hal/api/inc/halSegmentIterator.h:130:27: error: 'SegmentIteratorPtr' was not declared in this scope
.//../hal/api/inc/halSegmentIterator.h:130:69: error: expected primary-expression before 'genomePos'
     inline bool operator>(SegmentIteratorPtr segmentIt, hal_index_t genomePos) {
                                                                     ^
[0m[91mIn file included from .//../hal/api/inc/hal.h:65:0,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halBottomSegmentIterator.h:37:9: error: 'BottomSegmentIteratorPtr' does not name a type
         BottomSegmentIteratorPtr clone() const;
         ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h:42:25: error: 'BottomSegmentIteratorPtr' does not name a type
         void copy(const BottomSegmentIteratorPtr &botSegIt);
                         ^
.//../hal/api/inc/halBottomSegmentIterator.h:46:29: error: 'TopSegmentIteratorPtr' does not name a type
         void toParent(const TopSegmentIteratorPtr &topSegIt);
                             ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h:51:32: error: 'TopSegmentIteratorPtr' does not name a type
         void toParseDown(const TopSegmentIteratorPtr &topSegIt);
                                ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h:77:27: error: 'BottomSegmentIteratorPtr' does not name a type
         bool equals(const BottomSegmentIteratorPtr &other) const {
                           ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h:107:9: error: 'BottomSegmentPtr' does not name a type
         BottomSegmentPtr _bottomSegment;
         ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: In constructor 'hal::BottomSegmentIterator::BottomSegmentIterator(hal::BottomSegment*, hal_size_t, hal_size_t, bool)':
.//../hal/api/inc/halBottomSegmentIterator.h:29:66: error: class 'hal::BottomSegmentIterator' does not have any field named '_bottomSegment'
             : SegmentIterator(startOffset, endOffset, reversed), _bottomSegment(bottomSegment) {
                                                                  ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'hal::BottomSegment* hal::BottomSegmentIterator::getBottomSegment()':
.//../hal/api/inc/halBottomSegmentIterator.h:55:20: error: '_bottomSegment' was not declared in this scope
             return _bottomSegment.get();
                    ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'const hal::BottomSegment* hal::BottomSegmentIterator::getBottomSegment() const':
.//../hal/api/inc/halBottomSegmentIterator.h:60:20: error: '_bottomSegment' was not declared in this scope
             return _bottomSegment.get();
                    ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'hal::BottomSegment* hal::BottomSegmentIterator::bseg()':
.//../hal/api/inc/halBottomSegmentIterator.h:65:20: error: '_bottomSegment' was not declared in this scope
             return _bottomSegment.get();
                    ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'const hal::BottomSegment* hal::BottomSegmentIterator::bseg() const':
.//../hal/api/inc/halBottomSegmentIterator.h:70:20: error: '_bottomSegment' was not declared in this scope
             return _bottomSegment.get();
                    ^
[0m[91mIn file included from /usr/include/c++/5/cassert:43:0,
                 from .//../hal/api/inc/halBottomSegmentIterator.h:15,
                 from .//../hal/api/inc/hal.h:65,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'bool hal::BottomSegmentIterator::equals(const int&) const':
.//../hal/api/inc/halBottomSegmentIterator.h:78:20: error: '_bottomSegment' was not declared in this scope
             assert(_bottomSegment->getGenome() == other->getGenome());
                    ^
.//../hal/api/inc/halBottomSegmentIterator.h:78:56: error: base operand of '->' is not a pointer
             assert(_bottomSegment->getGenome() == other->getGenome());
                                                        ^
[0m[91mIn file included from .//../hal/api/inc/hal.h:65:0,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halBottomSegmentIterator.h:79:44: error: base operand of '->' is not a pointer
             return getArrayIndex() == other->getArrayIndex();
                                            ^
[0m[91mIn file included from /usr/include/c++/5/cassert:43:0,
                 from .//../hal/api/inc/halBottomSegmentIterator.h:15,
                 from .//../hal/api/inc/hal.h:65,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'bool hal::BottomSegmentIterator::operator==(const hal::BottomSegmentIterator&) const':
.//../hal/api/inc/halBottomSegmentIterator.h:84:20: error: '_bottomSegment' was not declared in this scope
             assert(_bottomSegment->getGenome() == other.getBottomSegment()->getGenome());
                    ^
[0m[91mIn file included from .//../hal/api/inc/hal.h:65:0,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'virtual hal::Segment* hal::BottomSegmentIterator::getSegment()':
.//../hal/api/inc/halBottomSegmentIterator.h:95:20: error: '_bottomSegment' was not declared in this scope
             return _bottomSegment.get();
                    ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: In member function 'virtual const hal::Segment* hal::BottomSegmentIterator::getSegment() const':
.//../hal/api/inc/halBottomSegmentIterator.h:98:20: error: '_bottomSegment' was not declared in this scope
             return _bottomSegment.get();
                    ^
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h: At global scope:
.//../hal/api/inc/halBottomSegmentIterator.h:110:28: error: declaration of 'operator==' as non-function
     inline bool operator==(BottomSegmentIteratorPtr p1, BottomSegmentIteratorPtr p2) {
                            ^
.//../hal/api/inc/halBottomSegmentIterator.h:110:28: error: 'BottomSegmentIteratorPtr' was not declared in this scope
[0m[91m.//../hal/api/inc/halBottomSegmentIterator.h:110:57: error: 'BottomSegmentIteratorPtr' was not declared in this scope
     inline bool operator==(BottomSegmentIteratorPtr p1, BottomSegmentIteratorPtr p2) {
                                                         ^
[0m[91mhal2sg.cpp:318:1: error: expected '}' at end of input
 }
 ^
[0m[91mIn file included from /usr/include/c++/5/vector:64:0,
                 from .//../hal/api/inc/halAlignment.h:13,
                 from .//../hal/api/inc/hal.h:62,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
/usr/include/c++/5/bits/stl_vector.h: In instantiation of 'void std::vector<_Tp, _Alloc>::_M_assign_dispatch(_Integer, _Integer, std::__true_type) [with _Integer = long int; _Tp = hal::Genome*; _Alloc = std::allocator<hal::Genome*>]':
/usr/include/c++/5/bits/stl_vector.h:516:22:   required from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = long int; _Tp = hal::Genome*; _Alloc = std::allocator<hal::Genome*>]'
.//../hal/api/inc/halGenome.h:195:50:   required from here
/usr/include/c++/5/bits/stl_vector.h:1326:25: error: invalid conversion from 'long int' to 'std::vector<hal::Genome*>::value_type {aka hal::Genome*}' [-fpermissive]
         { _M_fill_assign(__n, __val); }
                         ^
[0m[91mIn file included from /usr/include/c++/5/vector:69:0,
                 from .//../hal/api/inc/halAlignment.h:13,
                 from .//../hal/api/inc/hal.h:62,
                 from sgbuilder.h:10,
                 from hal2sg.cpp:13:
/usr/include/c++/5/bits/vector.tcc:225:5: note:   initializing argument 2 of 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = hal::Genome*; _Alloc = std::allocator<hal::Genome*>; std::size_t = long unsigned int; std::vector<_Tp, _Alloc>::value_type = hal::Genome*]'
     vector<_Tp, _Alloc>::
     ^
[0m[91mmake[1]: *** [hal2sg.o] Error 1
[0mMakefile:18: recipe for target 'hal2sg.o' failed
make[1]: Leaving directory '/hal2vg/deps/hal2sg'
Makefile:31: recipe for target 'deps/hal2sg/libhal2sg.a' failed
[91mmake: *** [deps/hal2sg/libhal2sg.a] Error 2
[0m
ComparativeGenomicsToolkit / hal2vg

Tried building the Dockerfile exited with error #14
