search

isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
178 stars 44 forks source link

Can't get tagged version 0.3.0 and 1d16f07 to compile with GCC 4.7.2 and GCC 4.9.3 on Linux #24

Closed andreas-wilm closed 8 years ago

andreas-wilm commented 8 years ago

Tried GCC 4.7.2 and GCC 4.9.3 on Linux and tagged version v0.3.0 as well as current master 1d16f07. Errors look similar:

git clone https://github.com/isovic/graphmap.git graphmap.git
cd graphmap.git
# alternativaly: git checkout v0.3.0

# modules compile fine
GCC=/opt/gcc-4.7.2/bin/gcc make modules

# but:
GCC=/opt/gcc-4.7.2/bin/gcc make
...
mkdir -p ./bin/Linux-x64/
/opt/gcc-4.7.2/bin/gcc -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -L"codebase/seqlib/src/libs/libdivsufsort-2.0.1/build/lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/index/index.o ./obj_linux/src/index/index_hash.o ./obj_linux/src/index/index_owler.o ./obj_linux/src/index/index_sa.o ./obj_linux/src/index/index_spaced_hash.o ./obj_linux/src/index/index_spaced_hash_fast.o ./obj_linux/src/owler/dpfilter.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/owler_data.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/main.o ./obj_linux/src/program_parameters.o -lpthread -lgomp -lm -lz
./obj_linux/codebase/seqlib/src/libs/edlib.o: In function `std::_Vector_base<int, std::allocator<int> >::~_Vector_base()':
edlib.cpp:(.text._ZNSt12_Vector_baseIiSaIiEED2Ev[_ZNSt12_Vector_baseIiSaIiEED5Ev]+0x9): undefined reference to `operator delete(void*)'
./obj_linux/codebase/seqlib/src/libs/edlib.o: In function `_ZL23myersCalcEditDistanceNWPmiiPKhiS1_iiiPiS2_bPP13AlignmentDatai.isra.44':
edlib.cpp:(.text._ZL23myersCalcEditDistanceNWPmiiPKhiS1_iiiPiS2_bPP13AlignmentDatai.isra.44+0xe5): undefined reference to `operator new[](unsigned long)'
...

(full error message is 3MB!)
andreas-wilm commented 8 years ago

not reproducible