subwaystation
commented
1 year ago Could you please try to build the current master of odgi? This would help us to better debug your problem.
Open SomePersonSomeWhereInTheWorld opened 1 year ago
subwaystation
commented
1 year ago Could you please try to build the current master of odgi? This would help us to better debug your problem.
SomePersonSomeWhereInTheWorld
commented
1 year ago 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?
SomePersonSomeWhereInTheWorld
commented
1 year ago You use specifically
gmakeinstead 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 () {}.
pjotrp
commented
1 year ago These are C++ errors. Probably an old compiler.
SomePersonSomeWhereInTheWorld
commented
1 year ago These are C++ errors. Probably an old compiler.
gcc 13.0.1 and cmake 3.22.1 are old?
pjotrp
commented
1 year ago well then it is something else...
SomePersonSomeWhereInTheWorld
commented
1 year ago 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?