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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.base_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/alabaster.base.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘1.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alabaster.base’ can be installed ... OK
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.1/site-library/alabaster.base/libs/alabaster.base.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/alabaster.base.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base
###
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* 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::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]':
../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<Provisioner>(contents.get(), etrack, "", version);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/uzuki2/parse_json.hpp:578:28:   required from here
  578 |     parse<DummyProvisioner>(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<char>(((const char*)"levels"), std::allocator<char>()), (* & 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<char>(((const char*)"values"), std::allocator<char>()), (* & 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::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]':
../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<Provisioner>(contents.get(), etrack, "", version);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/uzuki2/parse_json.hpp:578:28:   required from here
  578 |     parse<DummyProvisioner>(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<char>(((const char*)"levels"), std::allocator<char>()), (* & 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<char>(((const char*)"values"), std::allocator<char>()), (* & path))'
  367 |         const auto& vals = extract_array(map, "values", path);
      |                            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
../inst/include/uzuki2/parse_json.hpp: In instantiation of 'std::shared_ptr<uzuki2::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = RProvisioner; Externals = uzuki2::ExternalTracker<RExternals>; std::string = std::__cxx11::basic_string<char>]':
../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<Provisioner>(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<char>]'
  500 |     return parse<Provisioner>(reader, std::move(ext), std::move(options));
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
load_list.cpp:413:54:   required from here
  413 |     auto ptr = uzuki2::json::parse_file<RProvisioner>(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<char>(((const char*)"levels"), std::allocator<char>()), (* & 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<char>(((const char*)"values"), std::allocator<char>()), (* & 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<char>(((const char*)"atomic_vector"), std::allocator<char>()))'
   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<char>(((const char*)"simple_list"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"simple_list"), std::allocator<char>()))'
   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<char>(((const char*)"simple_list"), std::allocator<char>()))'
  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<char>(((const char*)"data_frame"), std::allocator<char>()))'
  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<char>(((const char*)"data_frame_factor"), std::allocator<char>()))'
   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<char>(((const char*)"genomic_ranges"), std::allocator<char>()))'
   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<char>(((const char*)"compressed_sparse_matrix"), std::allocator<char>()))'
  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<char>(((const char*)"summarized_experiment"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))'
   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<char>(((const char*)"summarized_experiment"), std::allocator<char>()))'
  122 |     const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/takane/summarized_experiment.hpp: In function 'std::vector<long unsigned int> 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<char>(((const char*)"summarized_experiment"), std::allocator<char>()))'
  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<char>(((const char*)"ranged_summarized_experiment"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"ranged_summarized_experiment"), std::allocator<char>()))'
   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<char>(((const char*)"single_cell_experiment"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"single_cell_experiment"), std::allocator<char>()))'
   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<char>(((const char*)"spatial_experiment"), std::allocator<char>()))'
  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<char>(((const char*)"multi_sample_dataset"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"multi_sample_dataset"), std::allocator<char>()))'
   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<char>(((const char*)"sequence_string_set"), std::allocator<char>()))'
  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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"sequence_string_set"), std::allocator<char>()))'
  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<takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)> >((* & obj), std::__cxx11::basic_string<char>(((const char*)"sequence_type"), std::allocator<char>()), (<lambda closure object>takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>(), takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>()))'
  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<char>(((const char*)"sequence_string_set"), std::allocator<char>()))'
  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<char>(((const char*)"bam_file"), std::allocator<char>()))'
   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<char>(((const char*)"bcf_file"), std::allocator<char>()))'
   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<char>(((const char*)"bigwig_file"), std::allocator<char>()))'
   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<char>(((const char*)"bigbed_file"), std::allocator<char>()))'
   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<char>(((const char*)"fasta_file"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"fasta_file"), std::allocator<char>()))'
   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<char>(((const char*)"fastq_file"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"fastq_file"), std::allocator<char>()))'
   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<takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)> >((* & fqmap), std::__cxx11::basic_string<char>(((const char*)"quality_type"), std::allocator<char>()), (<lambda closure object>takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>(), takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>()))'
   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<char>(((const char*)"bed_file"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"bed_file"), std::allocator<char>()))'
   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<char>(((const char*)"gmt_file"), std::allocator<char>()))'
   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<char>(((const char*)"gff_file"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"gff_file"), std::allocator<char>()))'
   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<char>(((const char*)"format"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"gff_file"), std::allocator<char>()))'
   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<char>(((const char*)"rds_file"), std::allocator<char>()))'
   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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"rds_file"), std::allocator<char>()))'
   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<char>(((const char*)"vcf_experiment"), std::allocator<char>()))'
  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<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))'
  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<char>(((const char*)"vcf_experiment"), std::allocator<char>()))'
  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<long unsigned int> 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<char>(((const char*)"vcf_experiment"), std::allocator<char>()))'
  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::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]':
../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<Provisioner>(contents.get(), etrack, "", version);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/uzuki2/parse_json.hpp:578:28:   required from here
  578 |     parse<DummyProvisioner>(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<char>(((const char*)"levels"), std::allocator<char>()), (* & 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<char>(((const char*)"values"), std::allocator<char>()), (* & 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<long unsigned int>&, 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<long unsigned int>&, 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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> library(testthat)
> library(alabaster.base)
> test_check("alabaster.base")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 565 ]
> 
> proc.time()
   user  system elapsed 
 86.945   3.197  80.270