vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Compilation Error on OSX #2350

Closed robert-piecyk closed 5 years ago

robert-piecyk commented 5 years ago

Please describe:

  1. What you were trying to do I tried to compile the current master branch of vg toolkit.
  2. What you wanted to happen To finish the compilation successfully
  3. What actually happened
    . ./source_me.sh && /opt/local/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -msse4.2  -isystem /usr/local/include -I /usr/local/include/cairo -fopenmp -o bin/vg obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/convert_handle.o obj/unittest/dagify.o obj/unittest/distributions.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/gbwt_helper.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/indexed_vg.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/srpe_filter.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/benchmark_main.o obj/subcommand/bugs_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/compare_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/crash_main.o obj/subcommand/deconstruct_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gaffe_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/locify_main.o obj/subcommand/map_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o obj/subcommand/xg_main.o  -lvg -I/Users/piecyk/vg/include -I. -I/Users/piecyk/vg/src -I/Users/piecyk/vg/src/unittest -I/Users/piecyk/vg/src/subcommand -I/Users/piecyk/vg/include/dynamic -I/Users/piecyk/vg/include/sonLib -I/opt/local/include/cairo -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pixman-1 -I/opt/local/include -I/opt/local/include/ossp -I/opt/local/include/freetype2 -I/opt/local/include/libpng16 -I/opt/local/include -L/Users/piecyk/vg/lib /Users/piecyk/vg/lib/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw /Users/piecyk/vg/lib/libprotobuf.a -lsublinearLS /Users/piecyk/vg/lib/libhts.a /Users/piecyk/vg/lib/libdeflate.a -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lsglib -L/opt/local/lib -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -lintl -Wl,-framework -Wl,CoreFoundation -lpcre -lintl -Wl,-framework -Wl,CoreFoundation -liconv -Wl,-framework,Carbon -Wl,-framework,Foundation -Wl,-framework,AppKit -lpcre -D_THREAD_SAFE -lpixman-1 -lfontconfig -liconv -lexpat -luuid -lfreetype -lbz2 -lpng16 -lz -lX11-xcb -lxcb-render -lXrender -lXext -lX11 -lxcb -lXau -lXdmcp -ljansson -L/opt/local/lib -L/usr/local/lib -lcairo -ldl -llzma -lrocksdb  -lsnappy -lz -lbz2
    Undefined symbols for architecture x86_64:
    "rocksdb::NewLRUCache(unsigned long, int, bool, double, std::shared_ptr<rocksdb::MemoryAllocator>, bool)", referenced from:
      vg::Index::GetOptions(bool) in libvg.a(index.o)
    "rocksdb::kDefaultToAdaptiveMutex", referenced from:
      vg::Index::GetOptions(bool) in libvg.a(index.o)
    ld: symbol(s) not found for architecture x86_64
    collect2: error: ld returned 1 exit status
    make: *** [bin/vg] Error 1
  4. What data and command line to use to make the problem recur, if applicable
    
    . ./source_me.sh && make
robert-piecyk commented 5 years ago

Right now after updating the protobuf to the newest version this error occurs:

. ./source_me.sh && /opt/local/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -msse4.2  -isystem /usr/local/include -I /usr/local/include/cairo -fopenmp -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp -I/Users/piecyk/vg/include -I. -I/Users/piecyk/vg/src -I/Users/piecyk/vg/src/unittest -I/Users/piecyk/vg/src/subcommand -I/Users/piecyk/vg/include/dynamic -I/Users/piecyk/vg/include/sonLib -I/opt/local/include/cairo -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pixman-1 -I/opt/local/include -I/opt/local/include/ossp -I/opt/local/include/freetype2 -I/opt/local/include/libpng16 -I/opt/local/include 2>&1 | python /Users/piecyk/vg/scripts/filter-noisy-assembler-warnings.py
In file included from src/handle.hpp:19,
                 from src/banded_global_aligner.hpp:20,
                 from src/banded_global_aligner.cpp:8:
/Users/piecyk/vg/include/vg/vg.pb.h:17:2: error: #error This file was generated by an older version of protoc which is
   17 | #error This file was generated by an older version of protoc which is
      |  ^~~~~
/Users/piecyk/vg/include/vg/vg.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. Please
   18 | #error incompatible with your Protocol Buffer headers. Please
      |  ^~~~~
/Users/piecyk/vg/include/vg/vg.pb.h:19:2: error: #error regenerate this file with a newer version of protoc.
   19 | #error regenerate this file with a newer version of protoc.
      |  ^~~~~
make: *** [obj/banded_global_aligner.o] Error 1