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Official home of genome aligner based upon notion of Cactus graphs
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c++: fatal error: Killed signal terminated program cc1plus on build-tools/downloadPangenomeTools, odgi-v0.8.3, RHEL 8, c++ 10.2.0 #1106

Open SomePersonSomeWhereInTheWorld opened 1 year ago

SomePersonSomeWhereInTheWorld commented 1 year ago

Any fix for this? running: build-tools/downloadPangenomeTools

c++ --version
c++ (GCC) 10.2.0
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:132: CMakeFiles/odgi_objs.dir/src/algorithms/subgraph/region.cpp.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp: In function ‘void odgi::algorithms::add_full_paths_to_component(const odgi::graph_t&, odgi::graph_t&, uint64_t)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:36:36: error: found ‘:’ in nested-name-specifier, expected ‘::’
             for (auto& source_path : taken_source_paths) {
                                    ^
                                    ::
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:36:24: error: ‘source_path’ has not been declared
             for (auto& source_path : taken_source_paths) {
                        ^~~~~~~~~~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:36:56: error: qualified-id in declaration before ‘)’ token
             for (auto& source_path : taken_source_paths) {
                                                        ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:43:14: error: expected ‘;’ before ‘}’ token
             }
              ^
              ;
         }
         ~     
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:44:9: error: expected primary-expression before ‘}’ token
         }
         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:43:14: error: expected ‘;’ before ‘}’ token
             }
              ^
              ;
         }
         ~     
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:44:9: error: expected primary-expression before ‘}’ token
         }
         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:43:14: error: expected ‘)’ before ‘}’ token
             }
              ^
              )
         }
         ~     
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:36:17: note: to match this ‘(’
             for (auto& source_path : taken_source_paths) {
                 ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:44:9: error: expected primary-expression before ‘}’ token
         }
         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:36:13: error: expected iteration declaration or initialization
             for (auto& source_path : taken_source_paths) {
             ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp: In function ‘void odgi::algorithms::windows_in_out(const handlegraph::PathHandleGraph&, const std::vector<handlegraph::path_handle_t>&, const std::function<bool(handlegraph::handle_t)>&, const uint64_t&, const std::function<void(const std::vector<odgi::path_range_t>&)>&, const uint64_t&)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:406:37: error: found ‘:’ in nested-name-specifier, expected ‘::’
             for (path_handle_t path : paths) {
                                     ^
                                     ::
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:406:32: error: ‘path’ has not been declared
             for (path_handle_t path : paths) {
                                ^~~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:406:44: error: qualified-id in declaration before ‘)’ token
             for (path_handle_t path : paths) {
                                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:457:14: error: expected ‘;’ before ‘}’ token
             }
              ^
              ;
         }
         ~     
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:458:9: error: expected primary-expression before ‘}’ token
         }
         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:457:14: error: expected ‘;’ before ‘}’ token
             }
              ^
              ;
         }
         ~     
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:458:9: error: expected primary-expression before ‘}’ token
         }
         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:457:14: error: expected ‘)’ before ‘}’ token
             }
              ^
              )
         }
         ~     
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:406:17: note: to match this ‘(’
             for (path_handle_t path : paths) {
                 ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:458:9: error: expected primary-expression before ‘}’ token
         }
         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/algorithms/subgraph/extract.cpp:406:13: error: expected iteration declaration or initialization
             for (path_handle_t path : paths) {
             ^~~
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:76: CMakeFiles/odgi_objs.dir/src/odgi.cpp.o] Error 1
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:146: CMakeFiles/odgi_objs.dir/src/algorithms/subgraph/extract.cpp.o] Error 1
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp: In function ‘int odgi::main_overlap(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:157:40: error: found ‘:’ in nested-name-specifier, expected ‘::’
                 for (path_handle_t p_h : paths_to_consider) {
                                        ^
                                        ::
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:157:36: error: ‘p_h’ has not been declared
                 for (path_handle_t p_h : paths_to_consider) {
                                    ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:157:59: error: qualified-id in declaration before ‘)’ token
                 for (path_handle_t p_h : paths_to_consider) {
                                                           ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:171:18: error: expected ‘;’ before ‘std’
                 }
                  ^
                  ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:173:17:
                 std::sort(touched_path_handles.begin(), touched_path_handles.end(),
                 ~~~
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:118: CMakeFiles/odgi_objs.dir/src/utils.cpp.o] Error 1
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:179:17: error: expected primary-expression before ‘for’
                 for (auto touched_path_handle : touched_path_handles) {
                 ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:176:28: error: expected ‘)’ before ‘for’
                         });
                            ^
                            )
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:179:17:
                 for (auto touched_path_handle : touched_path_handles) {
                 ~~~         
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:157:21: note: to match this ‘(’
                 for (path_handle_t p_h : paths_to_consider) {
                     ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:183:13: error: expected primary-expression before ‘}’ token
             }
             ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/overlap_main.cpp:157:17: error: expected iteration declaration or initialization
                 for (path_handle_t p_h : paths_to_consider) {
                 ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp: In function ‘int odgi::main_depth(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:274:29: error: found ‘:’ in nested-name-specifier, expected ‘::’
             for (auto& path : paths) {
                             ^
                             ::
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:274:24: error: ‘path’ has not been declared
             for (auto& path : paths) {
                        ^~~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:274:36: error: qualified-id in declaration before ‘)’ token
             for (auto& path : paths) {
                                    ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected ‘;’ before end of line
 #pragma omp critical (cout)
                            ^
                            ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected primary-expression before end of line
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected ‘;’ before end of line
 #pragma omp critical (cout)
                            ^
                            ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected primary-expression before end of line
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected ‘)’ before end of line
 #pragma omp critical (cout)
                            ^
                            )
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:274:17: note: to match this ‘(’
             for (auto& path : paths) {
                 ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected primary-expression before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:274:13: error: expected iteration declaration or initialization
             for (auto& path : paths) {
             ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:264:32: note: to match this ‘{’
         } else if (path_depth) {
                                ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:17:43: note: to match this ‘{’
     int main_depth(int argc, char **argv) {
                                           ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp: At global scope:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:13:16: note: to match this ‘{’
 namespace odgi {
                ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: error: expected declaration before end of line
 #pragma omp critical (cout)
                            ^
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:258: CMakeFiles/odgi_objs.dir/src/subcommand/overlap_main.cpp.o] Error 1
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp: In function ‘int odgi::main_squeeze(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:194:40: error: found ‘:’ in nested-name-specifier, expected ‘::’
                 for (auto old_new_path : old_and_new_paths) {
                                        ^
                                        ::
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:194:27: error: ‘old_new_path’ has not been declared
                 for (auto old_new_path : old_and_new_paths) {
                           ^~~~~~~~~~~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:194:59: error: qualified-id in declaration before ‘)’ token
                 for (auto old_new_path : old_and_new_paths) {
                                                           ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:203:18: error: expected ‘;’ before ‘shift_id’
                 }
                  ^
                  ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:205:17:
                 shift_id = max_id;
                 ~~~~~~~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:206:35: error: expected ‘)’ before ‘;’ token
                 ++input_graph_rank;
                                   ^
                                   )
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:194:21: note: to match this ‘(’
                 for (auto old_new_path : old_and_new_paths) {
                     ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/squeeze_main.cpp:194:17: error: expected iteration declaration or initialization
                 for (auto old_new_path : old_and_new_paths) {
                 ^~~
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:272: CMakeFiles/odgi_objs.dir/src/unittest/driver.cpp.o] Error 1
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:286: CMakeFiles/odgi_objs.dir/src/unittest/handle.cpp.o] Error 1
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp: In function ‘int odgi::main_stats(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:787:25: error: expected ‘=’ before ‘:’ token
         for (auto& path : paths) {
                         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected ‘;’ before end of line
 #pragma omp critical (cout)
                            ^
                            ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected primary-expression before end of line
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected ‘;’ before end of line
 #pragma omp critical (cout)
                            ^
                            ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected primary-expression before end of line
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected ‘)’ before end of line
 #pragma omp critical (cout)
                            ^
                            )
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:787:13: note: to match this ‘(’
         for (auto& path : paths) {
             ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected primary-expression before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:787:9: error: invalid type for iteration variable ‘path’
         for (auto& path : paths) {
         ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:777:43: note: to match this ‘{’
     if (args::get(weighted_feedback_arc)) {
                                           ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:20:39: note: to match this ‘{’
 int main_stats(int argc, char** argv) {
                                       ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp: At global scope:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:16:16: note: to match this ‘{’
 namespace odgi {
                ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: error: expected declaration before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp: In function ‘int odgi::main_paths(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:115:18: error: found ‘:’ in nested-name-specifier, expected ‘::’
   for (auto path : paths) {
                  ^
                  ::
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:115:13: error: ‘path’ has not been declared
   for (auto path : paths) {
             ^~~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:115:25: error: qualified-id in declaration before ‘)’ token
   for (auto path : paths) {
                         ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected ‘;’ before end of line
 #pragma omp critical (cout)
                            ^
                            ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected primary-expression before end of line
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected ‘;’ before end of line
 #pragma omp critical (cout)
                            ^
                            ;
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected primary-expression before end of line
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected ‘)’ before end of line
 #pragma omp critical (cout)
                            ^
                            )
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:115:7: note: to match this ‘(’
   for (auto path : paths) {
       ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected primary-expression before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:115:3: error: expected iteration declaration or initialization
   for (auto path : paths) {
   ^~~
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:109:44: note: to match this ‘{’
     if (list_path_start_end && list_names) {
                                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:14:39: note: to match this ‘{’
 int main_paths(int argc, char** argv) {
                                       ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp: At global scope:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected ‘}’ before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:10:16: note: to match this ‘{’
 namespace odgi {
                ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: error: expected declaration before end of line
 #pragma omp critical (cout)
                            ^
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp: In function ‘int odgi::main_depth(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/depth_main.cpp:289:28: warning: control reaches end of non-void function [-Wreturn-type]
 #pragma omp critical (cout)
                            ^
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:244: CMakeFiles/odgi_objs.dir/src/subcommand/depth_main.cpp.o] Error 1
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:482: CMakeFiles/odgi_objs.dir/src/subcommand/squeeze_main.cpp.o] Error 1
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp: In function ‘int odgi::main_paths(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/paths_main.cpp:121:28: warning: control reaches end of non-void function [-Wreturn-type]
 #pragma omp critical (cout)
                            ^
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:566: CMakeFiles/odgi_objs.dir/src/subcommand/paths_main.cpp.o] Error 1
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp: In function ‘int odgi::main_stats(int, char**)’:
/myuser/cactus/build-pangenome-tools/odgi-v0.8.3/src/subcommand/stats_main.cpp:810:28: warning: control reaches end of non-void function [-Wreturn-type]
 #pragma omp critical (cout)
                            ^
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:440: CMakeFiles/odgi_objs.dir/src/subcommand/stats_main.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:831: CMakeFiles/odgi_objs.dir/all] Error 2
gmake: *** [Makefile:146: all] Error 2
glennhickey commented 1 year ago

Does it work if you run

export CXXFLAGS="-std=c++11"

first?

SomePersonSomeWhereInTheWorld commented 1 year ago

No, ends with the same exact error.

glennhickey commented 1 year ago

Sorry, I don't have much else to suggest. odgi's the last tool installed in downloadPangenomeTools so even with this error, you should get a working Cactus at the end (for everything but odgi).

The binary and docker releases do contain odgi and should work on most systems, so you can try those: https://github.com/ComparativeGenomicsToolkit/cactus/releases/tag/v2.6.4

But if you really want to build odgi from source, you're probably best to deal directly with odgi's github. I'm happy to incorporate any fixes you find there if possible into Cactus.