Make issue (solved)

[wdecoster]

Hi,

When building the latest release on CentOS6 I received the error below:

g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/gindex/src/main.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/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.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/tictoc.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/alignment/transcriptome_mod.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/graphmap/transcriptome.o ./obj_linux/src/index/index_util.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/owler.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 /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: ./obj_linux/codebase/seqlib/src/utility/tictoc.o: undefined reference to symbol 'clock_gettime@@GLIBC_2.2.5' /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: note: 'clock_gettime@@GLIBC_2.2.5' is defined in DSO /lib64/librt.so.1 so try adding it to the linker command line /lib64/librt.so.1: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make: *** [linux] Error 1

According to http://stackoverflow.com/questions/2418157/ubuntu-linux-c-error-undefined-reference-to-clock-gettime-and-clock-settim this can be solved by adding -lrt to the g++ command

So I added -lrt to line 120 in the Makefile, which solved the issue.