Open SomePersonSomeWhereInTheWorld opened 1 year ago
Could you please try to build the current master of odgi? This would help us to better debug your problem.
Could you please try to build the current master of odgi?
using cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic && cmake --build build -- -j 3
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- pybind11 v2.11.0 dev1
-- Configuring done
-- Generating done
-- Build files have been written to: /path/to/me/odgi/build
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp: In function ‘void odgi::algorithms::add_full_paths_to_component(const odgi::graph_t&, odgi::graph_t&, uint64_t)’:
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:36:36: error: found ‘:’ in nested-name-specifier, expected ‘::’
for (auto& source_path : taken_source_paths) {
^
::
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:36:24: error: ‘source_path’ has not been declared
for (auto& source_path : taken_source_paths) {
^~~~~~~~~~~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:36:56: error: qualified-id in declaration before ‘)’ token
for (auto& source_path : taken_source_paths) {
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:43:14: error: expected ‘;’ before ‘}’ token
}
^
;
}
~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:44:9: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:43:14: error: expected ‘;’ before ‘}’ token
}
^
;
}
~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:44:9: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:43:14: error: expected ‘)’ before ‘}’ token
}
^
)
}
~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:36:17: note: to match this ‘(’
for (auto& source_path : taken_source_paths) {
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:44:9: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:36:13: error: expected iteration declaration or initialization
for (auto& source_path : taken_source_paths) {
^~~
/path/to/me/odgi/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&)’:
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:406:37: error: found ‘:’ in nested-name-specifier, expected ‘::’
for (path_handle_t path : paths) {
^
::
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:406:32: error: ‘path’ has not been declared
for (path_handle_t path : paths) {
^~~~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:406:44: error: qualified-id in declaration before ‘)’ token
for (path_handle_t path : paths) {
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:457:14: error: expected ‘;’ before ‘}’ token
}
^
;
}
~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:458:9: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:457:14: error: expected ‘;’ before ‘}’ token
}
^
;
}
~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:458:9: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:457:14: error: expected ‘)’ before ‘}’ token
}
^
)
}
~
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:406:17: note: to match this ‘(’
for (path_handle_t path : paths) {
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:458:9: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/algorithms/subgraph/extract.cpp:406:13: error: expected iteration declaration or initialization
for (path_handle_t path : paths) {
^~~
/path/to/me/odgi/src/subcommand/depth_main.cpp: In function ‘int odgi::main_depth(int, char**)’:
/path/to/me/odgi/src/subcommand/depth_main.cpp:274:29: error: found ‘:’ in nested-name-specifier, expected ‘::’
for (auto& path : paths) {
^
::
/path/to/me/odgi/src/subcommand/depth_main.cpp:274:24: error: ‘path’ has not been declared
for (auto& path : paths) {
^~~~
/path/to/me/odgi/src/subcommand/depth_main.cpp:274:36: error: qualified-id in declaration before ‘)’ token
for (auto& path : paths) {
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected ‘;’ before end of line
#pragma omp critical (cout)
^
;
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected primary-expression before end of line
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected ‘;’ before end of line
#pragma omp critical (cout)
^
;
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected primary-expression before end of line
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected ‘)’ before end of line
#pragma omp critical (cout)
^
)
/path/to/me/odgi/src/subcommand/depth_main.cpp:274:17: note: to match this ‘(’
for (auto& path : paths) {
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected primary-expression before end of line
#pragma omp critical (cout)
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:274:13: error: expected iteration declaration or initialization
for (auto& path : paths) {
^~~
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected ‘}’ before end of line
#pragma omp critical (cout)
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:264:32: note: to match this ‘{’
} else if (path_depth) {
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected ‘}’ before end of line
#pragma omp critical (cout)
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:17:43: note: to match this ‘{’
int main_depth(int argc, char **argv) {
^
/path/to/me/odgi/src/subcommand/depth_main.cpp: At global scope:
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected ‘}’ before end of line
#pragma omp critical (cout)
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:13:16: note: to match this ‘{’
namespace odgi {
^
/path/to/me/odgi/src/subcommand/depth_main.cpp:289:28: error: expected declaration before end of line
#pragma omp critical (cout)
^
/path/to/me/odgi/src/subcommand/overlap_main.cpp: In function ‘int odgi::main_overlap(int, char**)’:
/path/to/me/odgi/src/subcommand/overlap_main.cpp:157:40: error: found ‘:’ in nested-name-specifier, expected ‘::’
for (path_handle_t p_h : paths_to_consider) {
^
::
/path/to/me/odgi/src/subcommand/overlap_main.cpp:157:36: error: ‘p_h’ has not been declared
for (path_handle_t p_h : paths_to_consider) {
^~~
/path/to/me/odgi/src/subcommand/overlap_main.cpp:157:59: error: qualified-id in declaration before ‘)’ token
for (path_handle_t p_h : paths_to_consider) {
^
/path/to/me/odgi/src/subcommand/overlap_main.cpp:171:18: error: expected ‘;’ before ‘std’
}
^
;
/path/to/me/odgi/src/subcommand/overlap_main.cpp:173:17:
std::sort(touched_path_handles.begin(), touched_path_handles.end(),
~~~
/path/to/me/odgi/src/subcommand/overlap_main.cpp:179:17: error: expected primary-expression before ‘for’
for (auto touched_path_handle : touched_path_handles) {
^~~
/path/to/me/odgi/src/subcommand/overlap_main.cpp:176:28: error: expected ‘)’ before ‘for’
});
^
)
/path/to/me/odgi/src/subcommand/overlap_main.cpp:179:17:
for (auto touched_path_handle : touched_path_handles) {
~~~
/path/to/me/odgi/src/subcommand/overlap_main.cpp:157:21: note: to match this ‘(’
for (path_handle_t p_h : paths_to_consider) {
^
/path/to/me/odgi/src/subcommand/overlap_main.cpp:183:13: error: expected primary-expression before ‘}’ token
}
^
/path/to/me/odgi/src/subcommand/overlap_main.cpp:157:17: error: expected iteration declaration or initialization
for (path_handle_t p_h : paths_to_consider) {
^~~
/path/to/me/odgi/src/subcommand/depth_main.cpp: In function ‘int odgi::main_depth(int, char**)’:
/path/to/me/odgi/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]: *** Waiting for unfinished jobs....
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:146: CMakeFiles/odgi_objs.dir/src/algorithms/subgraph/extract.cpp.o] Error 1
gmake[2]: *** [CMakeFiles/odgi_objs.dir/build.make:258: CMakeFiles/odgi_objs.dir/src/subcommand/overlap_main.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:831: CMakeFiles/odgi_objs.dir/all] Error 2
gmake: *** [Makefile:146: all] Error 2
You use specifically gmake
instead of make
. Maybe this is the issue? Else I have no idea. Maybe @pjotrp has some clue?
You use specifically
gmake
instead ofmake
. Maybe this is the issue?
When I tried gmake, that works fine, it's build-tools/downloadPangenomeTools that fails with all those syntax errors with () {}.
These are C++ errors. Probably an old compiler.
These are C++ errors. Probably an old compiler.
gcc 13.0.1 and cmake 3.22.1 are old?
well then it is something else...
Just to confirm I also used a newer gmake, same error:
~/.local/bin/make/bin/gmake --version
GNU Make 4.4
I created this issue over on the Cactus Git page. You can see the errors using gcc 10.3 and 13.0.1. Is there a fix for this that can be shared?