Closed haiwufan closed 6 years ago
kgururaj
commented
6 years ago Oops, this might be a problem from our side - can you try a temporary fix? In the file \<GenomicsDB>/CMakeLists.txt, can you comment out line 124 and try again in a fresh build directory? I'll fix this.
haiwufan
commented
6 years ago Hi Developer!
It dose not seem to work.
I comment out line 124 of GenomicsDB/CMakeLists.txt.
Then, I clean the directory of build, and recompile and make. There are some different error found.
$ cmake /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/work/Software/GenomicsDB-0.9.2
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test test_cpp_2011
-- Performing Test test_cpp_2011 - Success
-- Found MPI_C: /usr/lib64/openmpi3/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib64/openmpi3/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Performing Test OPENMPV4_FOUND
-- Performing Test OPENMPV4_FOUND - Failed
-- Found libuuid: /usr/include
-- Found RapidJSON: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/RapidJSON/include
-- Found htslib: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found OpenSSL: /usr/lib64/libcrypto.so (found version "1.0.2k")
-- Found libdbi: /usr/local/include
-- Performing Test LIBDBI_TEST_PROGRAM_COMPILES
-- Performing Test LIBDBI_TEST_PROGRAM_COMPILES - Success
-- Found Protobuf: /usr/local/include
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found Protobuf: /usr/local/lib/libprotobuf.a;-lpthread (found version "3.0.2")
-- Found libcsv: /usr/include
-- Found GTest: /usr/lib64/libgtest.so
-- Configuring done
-- Generating done
-- Build files have been written to: /work/Software/Download/Variant_Package/GenomicsDB/build
$ make -j8
Scanning dependencies of target TileDB
Scanning dependencies of target htslib
Scanning dependencies of target PROTOBUF_GENERATED_CXX_TARGET
[ 1%] Creating directories for 'TileDB'
[ 2%] Creating directories for 'htslib'
[ 3%] Running C++ protocol buffer compiler on genomicsdb_coordinates.proto
[ 5%] Running C++ protocol buffer compiler on genomicsdb_callsets_mapping.proto
[ 6%] Running C++ protocol buffer compiler on genomicsdb_export_config.proto
[ 7%] Running C++ protocol buffer compiler on genomicsdb_import_config.proto
[ 8%] Running C++ protocol buffer compiler on genomicsdb_vid_mapping.proto
[ 10%] No download step for 'TileDB'
[ 11%] No download step for 'htslib'
[ 11%] Built target PROTOBUF_GENERATED_CXX_TARGET
[ 12%] No patch step for 'htslib'
[ 13%] No patch step for 'TileDB'
[ 15%] No update step for 'TileDB'
[ 16%] Performing update step for 'htslib'
[ 17%] Performing configure step for 'TileDB'
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found libuuid: /usr/include
-- Found OpenSSL: /usr/lib64/libcrypto.so (found version "1.0.2k")
-- Found GTest: /usr/lib64/libgtest.so
make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule.
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen missing components: dot
-- Performing Test CXX_2011_FOUND
-- Performing Test CXX_2011_FOUND - Success
-- Compiler supports C++ 2011.
-- The TileDB library is compiled with verbosity.
-- Configuring done
-- Generating done
-- Build files have been written to: /work/Software/Download/Variant_Package/GenomicsDB/build/TileDB-prefix/src/TileDB-build
[ 18%] Performing build step for 'TileDB'
Scanning dependencies of target TILEDB_CORE_OBJECTS
[ 20%] Performing configure step for 'htslib'
[ 0%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o
[ 6%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o
[ 13%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o
[ 20%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o
[ 20%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o
[ 26%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o
[ 33%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o
[ 40%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o
checking for gcc... /usr/bin/cc
[ 40%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/cc accepts -g... yes
checking for /usr/bin/cc option to accept ISO C89... none needed
checking for ranlib... /usr/bin/ranlib
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... [ 46%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o
[ 53%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o
no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... [ 60%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o
[ 66%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o
/usr/bin/cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... [ 66%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o
yes
checking for sys/types.h... [ 73%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o
[ 80%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o
yes
checking for sys/stat.h... [ 86%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o
yes
checking for stdlib.h... [ 86%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o
yes
checking for string.h... [ 93%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o
yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
[ 93%] Built target TILEDB_CORE_OBJECTS
checking for library containing log... Scanning dependencies of target tiledb_shared
Scanning dependencies of target tiledb_static
[100%] Linking CXX static library libtiledb.a
[100%] Linking CXX shared library libtiledb.so
[100%] Built target tiledb_static
-lm
checking for zlib.h... [100%] Built target tiledb_shared
yes
checking for inflate in -lz... [ 21%] Performing install step for 'TileDB'
[ 93%] Built target TILEDB_CORE_OBJECTS
[ 93%] Built target tiledb_shared
[100%] Built target tiledb_static
Install the project...
-- Install configuration: "Release"
-- Installing: /work/Software/GenomicsDB-0.9.2/lib/libtiledb.a
yes
checking for library containing recv... none required
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... -- Installing: /work/Software/GenomicsDB-0.9.2/lib/libtiledb.so
-- Up-to-date: /work/Software/GenomicsDB-0.9.2/include/tiledb.h
-- Up-to-date: /work/Software/GenomicsDB-0.9.2/include/tiledb_constants.h
[ 22%] Completed 'TileDB'
yes
[ 22%] Built target TileDB
configure: creating ./config.status
Scanning dependencies of target GenomicsDB_library_object_files
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
[ 23%] Performing build step for 'htslib'
[ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o
[ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o
[ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o
[ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o
[ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o
[ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o
[ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o
[ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o
[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_query_config.cc.o
[ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o
[ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o
[ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o
[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o
[ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o
[ 42%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o
[ 43%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o
[ 45%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o
[ 46%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o
[ 47%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/command_line.cc.o
[ 48%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o
[ 50%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o
[ 51%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/json_config.cc.o
[ 52%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o
[ 53%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o
[ 55%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o
[ 56%] No install step for 'htslib'
[ 57%] Completed 'htslib'
[ 57%] Built target htslib
[ 58%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o
[ 60%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o
[ 61%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o
[ 62%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o
[ 63%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o
[ 65%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o
[ 66%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir//resources/genomicsdb_coordinates.pb.cc.o
[ 67%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir//resources/genomicsdb_callsets_mapping.pb.cc.o
[ 68%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir//resources/genomicsdb_export_config.pb.cc.o
[ 70%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o
[ 71%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir//resources/genomicsdb_vid_mapping.pb.cc.o
[ 71%] Built target GenomicsDB_library_object_files
Scanning dependencies of target genomicsdb
Scanning dependencies of target tiledbgenomicsdb
[ 72%] Linking CXX static library libgenomicsdb.a
[ 73%] Linking CXX shared library libtiledbgenomicsdb.so
[ 73%] Built target genomicsdb
Scanning dependencies of target runAllGTests
Scanning dependencies of target vcfdiff
Scanning dependencies of target vcf2tiledb
Scanning dependencies of target gt_mpi_gather
Scanning dependencies of target create_tiledb_workspace
Scanning dependencies of target vcf_histogram
Scanning dependencies of target consolidate_tiledb_array
[ 75%] Building CXX object src/test/cpp/src/CMakeFiles/runAllGTests.dir/main_testall.cc.o
[ 76%] Building CXX object tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o
[ 77%] Building CXX object tools/CMakeFiles/vcf2tiledb.dir/src/vcf2tiledb.cc.o
[ 78%] Building CXX object tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o
[ 80%] Building CXX object tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o
[ 81%] Building CXX object tools/CMakeFiles/create_tiledb_workspace.dir/src/create_tiledb_workspace.cc.o
[ 82%] Building CXX object tools/CMakeFiles/consolidate_tiledb_array.dir/src/consolidate_tiledb_array.cc.o
[ 83%] Building CXX object src/test/cpp/src/CMakeFiles/runAllGTests.dir/test_non_diploid_mapper.cc.o
[ 83%] Built target tiledbgenomicsdb
Scanning dependencies of target test_genomicsdb_bcf_generator
[ 85%] Building CXX object example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o
[ 86%] Linking CXX executable vcf_histogram
[ 87%] Linking CXX executable consolidate_tiledb_array
/usr/bin/ld: warning: libdbi.so.0, needed by /lib64/dbd/libdbdpgsql.so, may conflict with libdbi.so.1
[ 87%] Built target vcf_histogram
[ 88%] Linking CXX executable create_tiledb_workspace
Scanning dependencies of target test_genomicsdb_importer
[ 90%] Building CXX object example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o
[ 91%] Linking CXX executable test_genomicsdb_bcf_generator
/usr/bin/ld: warning: libdbi.so.0, needed by /lib64/dbd/libdbdpgsql.so, may conflict with libdbi.so.1
[ 91%] Built target consolidate_tiledb_array
[ 92%] Building CXX object src/test/cpp/src/CMakeFiles/runAllGTests.dir/test_multid_vector.cc.o
/usr/bin/ld: warning: libdbi.so.0, needed by /lib64/dbd/libdbdpgsql.so, may conflict with libdbi.so.1
[ 92%] Built target create_tiledb_workspace
[ 93%] Building CXX object src/test/cpp/src/CMakeFiles/runAllGTests.dir/test_mapping_data_loader.cc.o
/usr/bin/ld: warning: libdbi.so.0, needed by /lib64/dbd/libdbdpgsql.so, may conflict with libdbi.so.1
[ 93%] Built target test_genomicsdb_bcf_generator
[ 95%] Linking CXX executable gt_mpi_gather
[ 96%] Linking CXX executable vcf2tiledb
/usr/bin/ld: warning: libdbi.so.0, needed by /lib64/dbd/libdbdpgsql.so, may conflict with libdbi.so.1
[ 96%] Built target gt_mpi_gather
In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/test/cpp/src/test_mapping_data_loader.cc:23:0:
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/test/cpp/include/test_mapping_data_loader.h:39:17: error: ‘ContigInfo’ was not declared in this scope
std::vector
kgururaj
commented
6 years ago I forgot about the tests - can you comment out the block of lines 121-125 and retry? Sorry, this is cumbersome and we'll fix it
haiwufan
commented
6 years ago Thanks kgururaj. I comment out 121-125 lines, then "make -j8 " with no error.
kgururaj
commented
6 years ago Closing since the fix is incorporated into the master
Hi Developer! I meet some Error when I install GenomicsDB according to the https://github.com/Intel-HLS/GenomicsDB/wiki/Compiling-GenomicsDB.
Server system is centos 7.2, and gcc version is 7.2.1.
Install history and log as follow:
$ git clone --recursive https://github.com/Intel-HLS/GenomicsDB.git $ mkdir -p build $ cd build $ cmake /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB-DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/work/Software/GenomicsDB-0.9.2 -- The C compiler identification is GNU 7.2.1 -- The CXX compiler identification is GNU 7.2.1 -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Performing Test test_cpp_2011 -- Performing Test test_cpp_2011 - Success -- Found MPI_C: /usr/lib64/mpich-3.2/lib/libmpi.so
-- Found MPI_CXX: /usr/lib64/mpich-3.2/lib/libmpicxx.so;/usr/lib64/mpich-3.2/lib/libmpi.so
-- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Performing Test OPENMPV4_FOUND -- Performing Test OPENMPV4_FOUND - Success -- Found libuuid: /usr/include
-- Found RapidJSON: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/RapidJSON/include
-- Found htslib: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") -- Found OpenSSL: /usr/lib64/libssl.so;/usr/lib64/libcrypto.so (found version "1.0.2k") -- Found libdbi: /usr/local/include
-- Performing Test LIBDBI_TEST_PROGRAM_COMPILES -- Performing Test LIBDBI_TEST_PROGRAM_COMPILES - Success -- Found Protobuf: /usr/include
-- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE
-- Found PROTOBUF: /usr/lib64/libprotobuf.so
-- Found libcsv: /usr/include
-- Found GTest: /usr/lib64/libgtest.so
-- Configuring done -- Generating done -- Build files have been written to: /work/Software/Download/Variant_Package/GenomicsDB/build
$ make -j8
Scanning dependencies of target TileDB Scanning dependencies of target htslib Scanning dependencies of target PROTOBUF_GENERATED_CXX_TARGET [ 1%] [ 2%] [ 4%] Creating directories for 'htslib' Creating directories for 'TileDB' Running C++ protocol buffer compiler on genomicsdb_coordinates.proto [ 5%] [ 7%] Running C++ protocol buffer compiler on genomicsdb_callsets_mapping.proto [ 8%] [ 10%] No download step for 'htslib' Running C++ protocol buffer compiler on genomicsdb_export_config.proto Running C++ protocol buffer compiler on genomicsdb_import_config.proto [ 11%] [ 13%] [ 14%] [ 15%] Running C++ protocol buffer compiler on genomicsdb_vid_mapping.proto No patch step for 'htslib' No download step for 'TileDB' Performing update step for 'htslib' [ 15%] Built target PROTOBUF_GENERATED_CXX_TARGET [ 17%] [ 18%] No patch step for 'TileDB' No update step for 'TileDB' [ 20%] Performing configure step for 'TileDB' -- The C compiler identification is GNU 7.2.1 -- The CXX compiler identification is GNU 7.2.1 -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") -- Found libuuid: /usr/include
-- Found OpenSSL: /usr/lib64/libssl.so;/usr/lib64/libcrypto.so (found version "1.0.2k") -- Found GTest: /usr/lib64/libgtest.so
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
-- Performing Test CXX_2011_FOUND -- Performing Test CXX_2011_FOUND - Success -- Compiler supports C++ 2011. -- The TileDB library is compiled with verbosity. -- Configuring done -- Generating done -- Build files have been written to: /work/Software/Download/Variant_Package/GenomicsDB/build/TileDB-prefix/src/TileDB-build [ 21%] Performing build step for 'TileDB' Scanning dependencies of target TILEDB_CORE_OBJECTS [ 5%] [ 10%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o [ 15%] [ 21%] [ 26%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o [ 31%] [ 36%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o [ 23%] Performing configure step for 'htslib' [ 42%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o [ 47%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o checking for gcc... /opt/rh/devtoolset-7/root/usr/bin/cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... 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Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o no [ 63%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o checking shared library type for unknown-Linux... plain .so checking how to run the C preprocessor... /opt/rh/devtoolset-7/root/usr/bin/cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... [ 68%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o [ 73%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o [ 78%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o [ 84%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o yes [ 89%] checking for sys/types.h... Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o [ 94%] Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o [100%] yes Building CXX object core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes [100%] Built target TILEDB_CORE_OBJECTS checking for unistd.h... (cached) yes Scanning dependencies of target tiledb_shared Scanning dependencies of target tiledb_static Linking CXX shared library libtiledb.so Linking CXX static library libtiledb.a checking for sys/param.h... [100%] Built target tiledb_static [100%] yes Built target tiledb_shared checking for getpagesize... [ 24%] Performing install step for 'TileDB' yes checking for working mmap... [100%] Built target TILEDB_CORE_OBJECTS [100%] yes [100%] Built target tiledb_shared Built target tiledb_static checking for gmtime_r... Install the project... -- Install configuration: "Release" -- Installing: /work/Software/GenomicsDB-0.9.2/lib/libtiledb.a -- Installing: /work/Software/GenomicsDB-0.9.2/lib/libtiledb.so -- Up-to-date: /work/Software/GenomicsDB-0.9.2/include/tiledb_constants.h -- Up-to-date: /work/Software/GenomicsDB-0.9.2/include/tiledb.h [ 26%] Completed 'TileDB' yes [ 26%] checking for fsync... Built target TileDB Scanning dependencies of target GenomicsDB_library_object_files yes checking for drand48... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... [ 27%] [ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o yes checking for library containing recv... [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o [ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o [ 33%] [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o [ 36%] none required configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o [ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_query_config.cc.o config.status: creating htslib.pc.tmp config.status: creating config.h [ 40%] Performing build step for 'htslib' [ 42%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o [ 43%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o [ 44%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o [ 46%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o [ 47%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o [ 49%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o [ 50%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o [ 52%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o [ 53%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o [ 55%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/command_line.cc.o [ 56%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o [ 57%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o [ 59%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/json_config.cc.o [ 60%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o [ 62%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o [ 63%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o [ 65%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o [ 66%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o [ 68%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc: In member function ‘int SQLBasedVidMapper::load_field_info()’: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:180:11: error: ‘class FieldInfo’ has no member named ‘m_type_index’ ref.m_type_index = (iter).second; ^
~~~ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:186:11: error: ‘class FieldInfo’ has no member named ‘m_bcf_ht_type’; did you mean ‘m_vcf_type’? ref.m_bcf_ht_type = (iter).second; ^~~~~ m_vcf_type /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:206:35: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘unsigned int’) ref.m_length_descriptor = length_descriptor; ^~~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘unsigned int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘unsigned int’ to ‘FieldLengthDescriptor&&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:208:15: error: ‘class FieldInfo’ has no member named ‘m_num_elements’ ref.m_num_elements = KnownFieldInfo::get_num_elements_for_known_field_enum(known_field_enum, 0u, 0u); ^~~~~~ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:211:13: error: ‘class FieldInfo’ has no member named ‘m_num_elements’ ref.m_num_elements = 1; ^~~~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/vcf/vcf.h:35:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:27, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib/htslib/vcf.h:75:22: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’)define BCF_VL_FIXED 0 // variable length
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:212:35: note: in expansion of macro ‘BCF_VL_FIXED’ ref.m_length_descriptor = BCF_VL_FIXED; ^
~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘FieldLengthDescriptor&&’ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/vcf/vcf.h:35:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:27, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib/htslib/vcf.h:75:22: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’)define BCF_VL_FIXED 0 // variable length
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:216:35: note: in expansion of macro ‘BCF_VL_FIXED’ ref.m_length_descriptor = BCF_VL_FIXED; ^
~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘FieldLengthDescriptor&&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:217:13: error: ‘class FieldInfo’ has no member named ‘m_num_elements’ ref.m_num_elements = dbi_result_get_int(result, DBTABLE_FIELD_COLUMN_LENVAL.c_str()); ^~~~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/vcf/vcf.h:35:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:27, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib/htslib/vcf.h:77:22: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’)define BCF_VL_A 2
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:220:39: note: in expansion of macro ‘BCF_VL_A’ ref.m_length_descriptor = BCF_VL_A; ^
~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘FieldLengthDescriptor&&’ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/vcf/vcf.h:35:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:27, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib/htslib/vcf.h:78:22: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’)define BCF_VL_G 3
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:222:39: note: in expansion of macro ‘BCF_VL_G’ ref.m_length_descriptor = BCF_VL_G; ^
~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘FieldLengthDescriptor&&’ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/vcf/vcf.h:35:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:27, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib/htslib/vcf.h:79:22: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’)define BCF_VL_R 4
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:224:39: note: in expansion of macro ‘BCF_VL_R’ ref.m_length_descriptor = BCF_VL_R; ^
~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘FieldLengthDescriptor&&’ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/vcf/vcf.h:35:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:27, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/dependencies/htslib/htslib/vcf.h:76:22: error: no match for ‘operator=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’)define BCF_VL_VAR 1
/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:227:41: note: in expansion of macro ‘BCF_VL_VAR’ ref.m_length_descriptor = BCF_VL_VAR; ^
~~~~~ In file included from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper_sql.h:26:0, from /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:24: /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(const FieldLengthDescriptor&) class FieldLengthDescriptor ^~~~~/work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘const FieldLengthDescriptor&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: candidate: FieldLengthDescriptor& FieldLengthDescriptor::operator=(FieldLengthDescriptor&&) /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/include/utils/vid_mapper.h:175:7: note: no known conversion for argument 1 from ‘int’ to ‘FieldLengthDescriptor&&’ /work/Software/Download/Variant_Package/GenomicsDB/GenomicsDB/src/main/cpp/src/utils/vid_mapper_sql.cc:249:148: error: no match for ‘operator!=’ (operand types are ‘FieldLengthDescriptor’ and ‘int’) if ((ref.m_VCF_field_combine_operation == VCFFieldCombineOperationEnum::VCF_FIELD_COMBINE_OPERATION_CONCATENATE) && (ref.m_length_descriptor != BCF_VL_VAR)) { [ 69%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o make[2]: [src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o] Error 1 make[2]: Waiting for unfinished jobs.... make[1]: [src/main/CMakeFiles/GenomicsDB_library_object_files.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... [ 71%] No install step for 'htslib' [ 72%] Completed 'htslib' [ 72%] Built target htslib make: *** [all] Error 2How could I resolve this error?