############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘alabaster.base’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c check_csv.cpp -o check_csv.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c check_list.cpp -o check_list.o In file included from ../inst/include/uzuki2/uzuki2.hpp:17, from check_list.cpp:3: ../inst/include/uzuki2/parse_json.hpp: In instantiation of 'std::shared_ptr uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_json.hpp:450:44: required from 'uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals]' 450 | auto output = parse_object(contents.get(), etrack, "", version); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:578:28: required from here 578 | parse(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 236 | const auto& lvals = extract_array(map, "levels", path); | ^~~~~ ../inst/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"levels"), std::allocator()), (* & path))' 236 | const auto& lvals = extract_array(map, "levels", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 367 | const auto& vals = extract_array(map, "values", path); | ^~~~ ../inst/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"values"), std::allocator()), (* & path))' 367 | const auto& vals = extract_array(map, "values", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c is_rfc3339.cpp -o is_rfc3339.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c load_csv.cpp -o load_csv.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c load_list.cpp -o load_list.o In file included from ../inst/include/uzuki2/uzuki2.hpp:17, from load_list.cpp:3: ../inst/include/uzuki2/parse_json.hpp: In instantiation of 'std::shared_ptr uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_json.hpp:450:44: required from 'uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals]' 450 | auto output = parse_object(contents.get(), etrack, "", version); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:578:28: required from here 578 | parse(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 236 | const auto& lvals = extract_array(map, "levels", path); | ^~~~~ ../inst/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"levels"), std::allocator()), (* & path))' 236 | const auto& lvals = extract_array(map, "levels", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 367 | const auto& vals = extract_array(map, "values", path); | ^~~~ ../inst/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"values"), std::allocator()), (* & path))' 367 | const auto& vals = extract_array(map, "values", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp: In instantiation of 'std::shared_ptr uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = RProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_json.hpp:450:44: required from 'uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = RProvisioner; Externals = RExternals]' 450 | auto output = parse_object(contents.get(), etrack, "", version); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:500:30: required from 'uzuki2::ParsedList uzuki2::json::parse_file(const std::string&, Externals, Options) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string]' 500 | return parse(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ load_list.cpp:413:54: required from here 413 | auto ptr = uzuki2::json::parse_file(file, std::move(others)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 236 | const auto& lvals = extract_array(map, "levels", path); | ^~~~~ ../inst/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"levels"), std::allocator()), (* & path))' 236 | const auto& lvals = extract_array(map, "levels", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 367 | const auto& vals = extract_array(map, "values", path); | ^~~~ ../inst/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"values"), std::allocator()), (* & path))' 367 | const auto& vals = extract_array(map, "values", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c validate.cpp -o validate.o In file included from ../inst/include/takane/_validate.hpp:10, from ../inst/include/takane/takane.hpp:4, from validate.cpp:2: ../inst/include/takane/atomic_vector.hpp: In function 'void takane::atomic_vector::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/atomic_vector.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 33 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "atomic_vector"); | ^~~~~~~ ../inst/include/takane/atomic_vector.hpp:33:66: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"atomic_vector"), std::allocator()))' 33 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "atomic_vector"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:12: ../inst/include/takane/simple_list.hpp: In function 'void takane::simple_list::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/simple_list.hpp:75:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 75 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list"); | ^~~~~~~ ../inst/include/takane/simple_list.hpp:75:76: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"simple_list"), std::allocator()))' 75 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/simple_list.hpp:77:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const std::string& vstring = internal_json::extract_string_from_typed_object(metamap, "version", "simple_list"); | ^~~~~~~ ../inst/include/takane/simple_list.hpp:77:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & metamap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"simple_list"), std::allocator()))' 77 | const std::string& vstring = internal_json::extract_string_from_typed_object(metamap, "version", "simple_list"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/simple_list.hpp: In function 'size_t takane::simple_list::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/simple_list.hpp:143:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 143 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list"); | ^~~~~~~ ../inst/include/takane/simple_list.hpp:143:76: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"simple_list"), std::allocator()))' 143 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:13: ../inst/include/takane/data_frame.hpp: In function 'void takane::data_frame::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/data_frame.hpp:161:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 161 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame"); | ^~~~~~~ ../inst/include/takane/data_frame.hpp:161:66: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"data_frame"), std::allocator()))' 161 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:14: ../inst/include/takane/data_frame_factor.hpp: In function 'void takane::data_frame_factor::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/data_frame_factor.hpp:48:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 48 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame_factor"); | ^~~~~~~ ../inst/include/takane/data_frame_factor.hpp:48:66: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"data_frame_factor"), std::allocator()))' 48 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame_factor"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:16: ../inst/include/takane/genomic_ranges.hpp: In function 'void takane::genomic_ranges::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/genomic_ranges.hpp:96:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 96 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "genomic_ranges"); | ^~~~~~~ ../inst/include/takane/genomic_ranges.hpp:96:66: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"genomic_ranges"), std::allocator()))' 96 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "genomic_ranges"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:21: ../inst/include/takane/compressed_sparse_matrix.hpp: In function 'void takane::compressed_sparse_matrix::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/compressed_sparse_matrix.hpp:169:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 169 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "compressed_sparse_matrix"); | ^~~~~~~ ../inst/include/takane/compressed_sparse_matrix.hpp:169:66: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"compressed_sparse_matrix"), std::allocator()))' 169 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "compressed_sparse_matrix"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:22: ../inst/include/takane/summarized_experiment.hpp: In function 'void takane::summarized_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/summarized_experiment.hpp:45:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 45 | const auto& semap = internal_json::extract_typed_object_from_metadata(metadata.other, "summarized_experiment"); | ^~~~~ ../inst/include/takane/summarized_experiment.hpp:45:74: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"summarized_experiment"), std::allocator()))' 45 | const auto& semap = internal_json::extract_typed_object_from_metadata(metadata.other, "summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/summarized_experiment.hpp:47:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 47 | const std::string& vstring = internal_json::extract_string_from_typed_object(semap, "version", "summarized_experiment"); | ^~~~~~~ ../inst/include/takane/summarized_experiment.hpp:47:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & semap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"summarized_experiment"), std::allocator()))' 47 | const std::string& vstring = internal_json::extract_string_from_typed_object(semap, "version", "summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/summarized_experiment.hpp: In function 'size_t takane::summarized_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/summarized_experiment.hpp:122:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 122 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ^~~~~ ../inst/include/takane/summarized_experiment.hpp:122:54: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"summarized_experiment"), std::allocator()))' 122 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/summarized_experiment.hpp: In function 'std::vector takane::summarized_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/summarized_experiment.hpp:135:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 135 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ^~~~~ ../inst/include/takane/summarized_experiment.hpp:135:54: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"summarized_experiment"), std::allocator()))' 135 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:23: ../inst/include/takane/ranged_summarized_experiment.hpp: In function 'void takane::ranged_summarized_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/ranged_summarized_experiment.hpp:44:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const auto& rsemap = internal_json::extract_typed_object_from_metadata(metadata.other, "ranged_summarized_experiment"); | ^~~~~~ ../inst/include/takane/ranged_summarized_experiment.hpp:44:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"ranged_summarized_experiment"), std::allocator()))' 44 | const auto& rsemap = internal_json::extract_typed_object_from_metadata(metadata.other, "ranged_summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/ranged_summarized_experiment.hpp:46:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 46 | const std::string& vstring = internal_json::extract_string_from_typed_object(rsemap, "version", "ranged_summarized_experiment"); | ^~~~~~~ ../inst/include/takane/ranged_summarized_experiment.hpp:46:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & rsemap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"ranged_summarized_experiment"), std::allocator()))' 46 | const std::string& vstring = internal_json::extract_string_from_typed_object(rsemap, "version", "ranged_summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:24: ../inst/include/takane/single_cell_experiment.hpp: In function 'void takane::single_cell_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/single_cell_experiment.hpp:49:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 49 | const auto& scemap = internal_json::extract_typed_object_from_metadata(metadata.other, "single_cell_experiment"); | ^~~~~~ ../inst/include/takane/single_cell_experiment.hpp:49:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"single_cell_experiment"), std::allocator()))' 49 | const auto& scemap = internal_json::extract_typed_object_from_metadata(metadata.other, "single_cell_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/single_cell_experiment.hpp:51:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 51 | const std::string& vstring = internal_json::extract_string_from_typed_object(scemap, "version", "single_cell_experiment"); | ^~~~~~~ ../inst/include/takane/single_cell_experiment.hpp:51:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & scemap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"single_cell_experiment"), std::allocator()))' 51 | const std::string& vstring = internal_json::extract_string_from_typed_object(scemap, "version", "single_cell_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:25: ../inst/include/takane/spatial_experiment.hpp: In function 'void takane::spatial_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/spatial_experiment.hpp:237:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 237 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "spatial_experiment"); | ^~~~~~~ ../inst/include/takane/spatial_experiment.hpp:237:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"spatial_experiment"), std::allocator()))' 237 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "spatial_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:26: ../inst/include/takane/multi_sample_dataset.hpp: In function 'void takane::multi_sample_dataset::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/multi_sample_dataset.hpp:42:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 42 | const auto& dmap = internal_json::extract_typed_object_from_metadata(metadata.other, "multi_sample_dataset"); | ^~~~ ../inst/include/takane/multi_sample_dataset.hpp:42:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"multi_sample_dataset"), std::allocator()))' 42 | const auto& dmap = internal_json::extract_typed_object_from_metadata(metadata.other, "multi_sample_dataset"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/multi_sample_dataset.hpp:44:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const std::string& vstring = internal_json::extract_string_from_typed_object(dmap, "version", "multi_sample_dataset"); | ^~~~~~~ ../inst/include/takane/multi_sample_dataset.hpp:44:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & dmap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"multi_sample_dataset"), std::allocator()))' 44 | const std::string& vstring = internal_json::extract_string_from_typed_object(dmap, "version", "multi_sample_dataset"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:27: ../inst/include/takane/sequence_string_set.hpp: In function 'void takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/sequence_string_set.hpp:215:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 215 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set"); | ^~~ ../inst/include/takane/sequence_string_set.hpp:215:72: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"sequence_string_set"), std::allocator()))' 215 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/sequence_string_set.hpp:216:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 216 | const auto& vstring = internal_json::extract_string_from_typed_object(obj, "version", "sequence_string_set"); | ^~~~~~~ ../inst/include/takane/sequence_string_set.hpp:216:74: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & obj), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"sequence_string_set"), std::allocator()))' 216 | const auto& vstring = internal_json::extract_string_from_typed_object(obj, "version", "sequence_string_set"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/sequence_string_set.hpp:245:28: warning: possibly dangling reference to a temporary [-Wdangling-reference] 245 | const std::string& stype = internal_json::extract_string(obj, "sequence_type", [&](std::exception& e) -> void { | ^~~~~ ../inst/include/takane/sequence_string_set.hpp:245:65: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string >((* & obj), std::__cxx11::basic_string(((const char*)"sequence_type"), std::allocator()), (takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::(), takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::()))' 245 | const std::string& stype = internal_json::extract_string(obj, "sequence_type", [&](std::exception& e) -> void { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 | throw std::runtime_error("failed to extract 'sequence_string_set.sequence_type' from the object metadata; " + std::string(e.what())); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 | }); | ~~ ../inst/include/takane/sequence_string_set.hpp: In function 'size_t takane::sequence_string_set::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/sequence_string_set.hpp:362:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 362 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set"); | ^~~ ../inst/include/takane/sequence_string_set.hpp:362:72: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"sequence_string_set"), std::allocator()))' 362 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:28: ../inst/include/takane/bam_file.hpp: In function 'void takane::bam_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/bam_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bam_file"); | ^~~~~~~ ../inst/include/takane/bam_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"bam_file"), std::allocator()))' 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bam_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:29: ../inst/include/takane/bcf_file.hpp: In function 'void takane::bcf_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/bcf_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bcf_file"); | ^~~~~~~ ../inst/include/takane/bcf_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"bcf_file"), std::allocator()))' 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bcf_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:30: ../inst/include/takane/bigwig_file.hpp: In function 'void takane::bigwig_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/bigwig_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigwig_file"); | ^~~~~~~ ../inst/include/takane/bigwig_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"bigwig_file"), std::allocator()))' 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigwig_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:31: ../inst/include/takane/bigbed_file.hpp: In function 'void takane::bigbed_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/bigbed_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigbed_file"); | ^~~~~~~ ../inst/include/takane/bigbed_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"bigbed_file"), std::allocator()))' 34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigbed_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:32: ../inst/include/takane/fasta_file.hpp: In function 'void takane::fasta_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/fasta_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 33 | const auto& famap = internal_json::extract_typed_object_from_metadata(metadata.other, "fasta_file"); | ^~~~~ ../inst/include/takane/fasta_file.hpp:33:74: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"fasta_file"), std::allocator()))' 33 | const auto& famap = internal_json::extract_typed_object_from_metadata(metadata.other, "fasta_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/fasta_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(famap, "version", "fasta_file"); | ^~~~~~~ ../inst/include/takane/fasta_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & famap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"fasta_file"), std::allocator()))' 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(famap, "version", "fasta_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:33: ../inst/include/takane/fastq_file.hpp: In function 'void takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/fastq_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 33 | const auto& fqmap = internal_json::extract_typed_object_from_metadata(metadata.other, "fastq_file"); | ^~~~~ ../inst/include/takane/fastq_file.hpp:33:74: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"fastq_file"), std::allocator()))' 33 | const auto& fqmap = internal_json::extract_typed_object_from_metadata(metadata.other, "fastq_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/fastq_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(fqmap, "version", "fastq_file"); | ^~~~~~~ ../inst/include/takane/fastq_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & fqmap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"fastq_file"), std::allocator()))' 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(fqmap, "version", "fastq_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/fastq_file.hpp:45:28: warning: possibly dangling reference to a temporary [-Wdangling-reference] 45 | const std::string& qtype = internal_json::extract_string(fqmap, "quality_type", [&](std::exception& e) -> void { | ^~~~~ ../inst/include/takane/fastq_file.hpp:45:65: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string >((* & fqmap), std::__cxx11::basic_string(((const char*)"quality_type"), std::allocator()), (takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::(), takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::()))' 45 | const std::string& qtype = internal_json::extract_string(fqmap, "quality_type", [&](std::exception& e) -> void { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | throw std::runtime_error("failed to extract 'fastq_file.quality_type' from the object metadata; " + std::string(e.what())); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 | }); | ~~ In file included from ../inst/include/takane/_validate.hpp:34: ../inst/include/takane/bed_file.hpp: In function 'void takane::bed_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/bed_file.hpp:34:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 34 | const auto& bedmap = internal_json::extract_typed_object_from_metadata(metadata.other, "bed_file"); | ^~~~~~ ../inst/include/takane/bed_file.hpp:34:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"bed_file"), std::allocator()))' 34 | const auto& bedmap = internal_json::extract_typed_object_from_metadata(metadata.other, "bed_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/bed_file.hpp:36:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 36 | const std::string& vstring = internal_json::extract_string_from_typed_object(bedmap, "version", "bed_file"); | ^~~~~~~ ../inst/include/takane/bed_file.hpp:36:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & bedmap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"bed_file"), std::allocator()))' 36 | const std::string& vstring = internal_json::extract_string_from_typed_object(bedmap, "version", "bed_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:35: ../inst/include/takane/gmt_file.hpp: In function 'void takane::gmt_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/gmt_file.hpp:33:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 33 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "gmt_file"); | ^~~~~~~ ../inst/include/takane/gmt_file.hpp:33:73: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"gmt_file"), std::allocator()))' 33 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "gmt_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:36: ../inst/include/takane/gff_file.hpp: In function 'void takane::gff_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/gff_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 33 | const auto& gffmap = internal_json::extract_typed_object_from_metadata(metadata.other, "gff_file"); | ^~~~~~ ../inst/include/takane/gff_file.hpp:33:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"gff_file"), std::allocator()))' 33 | const auto& gffmap = internal_json::extract_typed_object_from_metadata(metadata.other, "gff_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/gff_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(gffmap, "version", "gff_file"); | ^~~~~~~ ../inst/include/takane/gff_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & gffmap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"gff_file"), std::allocator()))' 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(gffmap, "version", "gff_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/gff_file.hpp:43:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 43 | const std::string& fstring = internal_json::extract_string_from_typed_object(gffmap, "format", "gff_file"); | ^~~~~~~ ../inst/include/takane/gff_file.hpp:43:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & gffmap), std::__cxx11::basic_string(((const char*)"format"), std::allocator()), std::__cxx11::basic_string(((const char*)"gff_file"), std::allocator()))' 43 | const std::string& fstring = internal_json::extract_string_from_typed_object(gffmap, "format", "gff_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:37: ../inst/include/takane/rds_file.hpp: In function 'void takane::rds_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/rds_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 33 | const auto& rdsmap = internal_json::extract_typed_object_from_metadata(metadata.other, "rds_file"); | ^~~~~~ ../inst/include/takane/rds_file.hpp:33:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"rds_file"), std::allocator()))' 33 | const auto& rdsmap = internal_json::extract_typed_object_from_metadata(metadata.other, "rds_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/rds_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(rdsmap, "version", "rds_file"); | ^~~~~~~ ../inst/include/takane/rds_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & rdsmap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"rds_file"), std::allocator()))' 35 | const std::string& vstring = internal_json::extract_string_from_typed_object(rdsmap, "version", "rds_file"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/takane/_validate.hpp:40: ../inst/include/takane/vcf_experiment.hpp: In function 'void takane::vcf_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/vcf_experiment.hpp:188:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 188 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ^~~~~~ ../inst/include/takane/vcf_experiment.hpp:188:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"vcf_experiment"), std::allocator()))' 188 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/vcf_experiment.hpp:190:24: warning: possibly dangling reference to a temporary [-Wdangling-reference] 190 | const std::string& vstring = internal_json::extract_string_from_typed_object(vcfmap, "version", "vcf_experiment"); | ^~~~~~~ ../inst/include/takane/vcf_experiment.hpp:190:81: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_string_from_typed_object((* & vcfmap), std::__cxx11::basic_string(((const char*)"version"), std::allocator()), std::__cxx11::basic_string(((const char*)"vcf_experiment"), std::allocator()))' 190 | const std::string& vstring = internal_json::extract_string_from_typed_object(vcfmap, "version", "vcf_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/vcf_experiment.hpp: In function 'size_t takane::vcf_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/vcf_experiment.hpp:239:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 239 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ^~~~~~ ../inst/include/takane/vcf_experiment.hpp:239:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"vcf_experiment"), std::allocator()))' 239 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/takane/vcf_experiment.hpp: In function 'std::vector takane::vcf_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)': ../inst/include/takane/vcf_experiment.hpp:251:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 251 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ^~~~~~ ../inst/include/takane/vcf_experiment.hpp:251:75: note: the temporary was destroyed at the end of the full expression 'takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"vcf_experiment"), std::allocator()))' 251 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/uzuki2/uzuki2.hpp:17, from ../inst/include/takane/simple_list.hpp:8: ../inst/include/uzuki2/parse_json.hpp: In instantiation of 'std::shared_ptr uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_json.hpp:450:44: required from 'uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals]' 450 | auto output = parse_object(contents.get(), etrack, "", version); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:578:28: required from here 578 | parse(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 236 | const auto& lvals = extract_array(map, "levels", path); | ^~~~~ ../inst/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"levels"), std::allocator()), (* & path))' 236 | const auto& lvals = extract_array(map, "levels", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../inst/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 367 | const auto& vals = extract_array(map, "values", path); | ^~~~ ../inst/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression 'uzuki2::json::extract_array((* & map), std::__cxx11::basic_string(((const char*)"values"), std::allocator()), (* & path))' 367 | const auto& vals = extract_array(map, "values", path); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/chihaya/validate.hpp:13, from ../inst/include/chihaya/chihaya.hpp:10, from ../inst/include/takane/utils_public.hpp:13, from ../inst/include/takane/_validate.hpp:9: ../inst/include/chihaya/sparse_matrix.hpp: In function 'void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = int]': ../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: 'previous' may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ ../inst/include/chihaya/sparse_matrix.hpp:45:16: note: 'previous' was declared here 45 | Index_ previous; | ^~~~~~~~ ../inst/include/chihaya/sparse_matrix.hpp: In function 'void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = long unsigned int]': ../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: 'previous' may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ ../inst/include/chihaya/sparse_matrix.hpp:45:16: note: 'previous' was declared here 45 | Index_ previous; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-alabaster.base/00new/alabaster.base/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (alabaster.base)