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build_failure.linux-64.yaml
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recipe_sha: abd321a497022feaaaa9e3428b461c51998b1389a7780219f2a10092039d764f # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |-
[ 35%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/reassign_states.cpp.o
[ 36%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/check_samples.cpp.o
[ 36%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/optimize_tree.cpp.o
[ 37%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/condense.cpp.o
[ 37%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Fitch_Sankoff.cpp.o
[ 38%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/main_load_tree.cpp.o
[ 38%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/priority_conflict_resolver.cpp.o
[ 39%] Building CXX object CMakeFiles/usher-sampled.dir/src/usher-sampled/driver/main.cpp.o
/opt/conda/conda-bld/usher_1717952675556/work/src/usher-sampled/driver/main.cpp: In function 'void leader_thread_optimization(Mutation_Annotated_Tree::Tree&, std::vector<std::vector<std::pair<long int, nuc_one_hot> > >&, std::atomic_size_t&, int&, size_t, FILE*, float, bool)':
/opt/conda/conda-bld/usher_1717952675556/work/src/usher-sampled/driver/main.cpp:159:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
159 | if(optimization_radius>tree.max_level){
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/opt/conda/conda-bld/usher_1717952675556/work/src/usher-sampled/driver/main.cpp: In function 'int leader_thread(int, Leader_Thread_Options&)':
/opt/conda/conda-bld/usher_1717952675556/work/src/usher-sampled/driver/main.cpp:250:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<nuc_one_hot>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
250 | for (int position=1; position<MAT::Mutation::refs.size(); position) {
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 39%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/apply_move.cpp.o
[ 40%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/backward_pass.cpp.o
[ 40%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/debug.cpp.o
[ 41%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/forward_pass.cpp.o
[ 41%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/move_node_no_reassign.cpp.o
[ 42%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/one_level_fitch_sankoff.cpp.o
[ 42%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/apply_move/one_level_fitch_sankoff_binary.cpp.o
[ 43%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/Profitable_Moves_Enumerator.cpp.o
[ 43%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/Profitable_Moves_Enumerators-debug.cpp.o
[ 44%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/check_move_profitable.cpp.o
[ 44%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/check_move_profitable_LCA.cpp.o
[ 45%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/check_move_profitable_dst_branch.cpp.o
[ 45%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/downward_integrated.cpp.o
[ 46%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/possible_change.cpp.o
[ 46%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/process_LCA.cpp.o
[ 47%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/process_inidividual_mutation.cpp.o
[ 47%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/process_intermediate_node.cpp.o
[ 48%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/process_terminal_nodes.cpp.o
[ 48%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/range_tree.cpp.o
[ 49%] Building CXX object CMakeFiles/usher-sampled.dir/src/matOptimize/Profitable_Moves_Enumerators/upward_integrated.cpp.o
[ 50%] Linking CXX executable usher-sampled
[ 51%] Built target usher-sampled
[ 51%] Building CXX object CMakeFiles/ripplesUtils.dir/src/mutation_annotated_tree.cpp.o
[ 52%] Building CXX object CMakeFiles/ripplesUtils.dir/src/usher_mapper.cpp.o
[ 53%] Building CXX object CMakeFiles/ripplesUtils.dir/src/matUtils/describe.cpp.o
[ 53%] Building CXX object CMakeFiles/ripplesUtils.dir/src/ripples/util/extract_formats.cpp.o
[ 54%] Building CXX object CMakeFiles/ripplesUtils.dir/src/ripples/util/parse_data.cpp.o
[ 54%] Building CXX object CMakeFiles/ripplesUtils.dir/src/ripples/util/ripplesUtils.cpp.o
[ 55%] Building CXX object CMakeFiles/ripplesUtils.dir/src/ripples/util/text_parser.cpp.o
[ 55%] Building CXX object CMakeFiles/ripplesUtils.dir/parsimony.pb.cc.o
[ 56%] Linking CXX executable ripplesUtils
[ 57%] Built target ripplesUtils
[ 58%] Building CXX object CMakeFiles/ripplesInit.dir/src/mutation_annotated_tree.cpp.o
[ 58%] Building CXX object CMakeFiles/ripplesInit.dir/src/usher_mapper.cpp.o
[ 59%] Building CXX object CMakeFiles/ripplesInit.dir/src/ripples/init/init_pipeline.cpp.o
[ 59%] Building CXX object CMakeFiles/ripplesInit.dir/src/ripples/init/main.cpp.o
[ 60%] Building CXX object CMakeFiles/ripplesInit.dir/parsimony.pb.cc.o
[ 60%] Linking CXX executable ripplesInit
[ 60%] Built target ripplesInit
[ 60%] Building CXX object CMakeFiles/compareVCF.dir/src/mutation_annotated_tree.cpp.o
[ 61%] Building CXX object CMakeFiles/compareVCF.dir/src/compareVCF.cpp.o
[ 61%] Building CXX object CMakeFiles/compareVCF.dir/src/usher_mapper.cpp.o
[ 62%] Building CXX object CMakeFiles/compareVCF.dir/parsimony.pb.cc.o
[ 62%] Linking CXX executable compareVCF
[ 63%] Built target compareVCF
[ 64%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/mutation_annotated_tree.cpp.o
[ 64%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/mutation_annotated_tree_node.cpp.o
[ 65%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/mutation_annotated_tree_load_store.cpp.o
[ 65%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/detailed_mutations_store.cpp.o
[ 66%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/detailed_mutations_load.cpp.o
[ 66%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/mutation_annotated_tree_nuc_util.cpp.o
[ 67%] Building CXX object CMakeFiles/matOptimize.dir/src/matOptimize/main.cpp.o
/opt/conda/conda-bld/usher_1717952675556/work/src/matOptimize/main.cpp: In function 'int main(int, char**)':
/opt/conda/conda-bld/usher_1717952675556/work/src/matOptimize/main.cpp:249:58: error: expected unqualified-id before '&' token
249 | } catch(const boost::filesystem::filesystem_error& ex) {
| ^
/opt/conda/conda-bld/usher_1717952675556/work/src/matOptimize/main.cpp:249:58: error: expected ')' before '&' token
249 | } catch(const boost::filesystem::filesystem_error& ex) {
| ~ ^
| )
/opt/conda/conda-bld/usher_1717952675556/work/src/matOptimize/main.cpp:249:58: error: expected '{' before '&' token
/opt/conda/conda-bld/usher_1717952675556/work/src/matOptimize/main.cpp:249:60: error: 'ex' was not declared in this scope; did you mean 'exp'?
249 | } catch(const boost::filesystem::filesystem_error& ex) {
| ^~
| exp
make[2]: *** [CMakeFiles/matOptimize.dir/build.make:176: CMakeFiles/matOptimize.dir/src/matOptimize/main.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:317: CMakeFiles/matOptimize.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
utils.check_call_env(
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/usher_1717952675556/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.
category: |-
compiler error