Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 41/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
alabaster.base 1.7.2 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the alabaster.base package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: alabaster.base |
Version: 1.7.2 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base |
StartedAt: 2024-12-22 19:49:38 -0000 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 19:51:48 -0000 (Sun, 22 Dec 2024) |
EllapsedTime: 130.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘alabaster.base’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++17 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c check_csv.cpp -o check_csv.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c check_list.cpp -o check_list.o In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/uzuki2.hpp:17, from check_list.cpp:3: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:578:28: required from here 578 | parse<DummyProvisioner>(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c is_rfc3339.cpp -o is_rfc3339.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c load_csv.cpp -o load_csv.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c load_list.cpp -o load_list.o In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/uzuki2.hpp:17, from load_list.cpp:3: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:578:28: required from here 578 | parse<DummyProvisioner>(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c validate.cpp -o validate.o In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:10, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/takane.hpp:4, from validate.cpp:2: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/atomic_vector.hpp: In function ‘void takane::atomic_vector::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:12: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp: In function ‘void takane::simple_list::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp: In function ‘size_t takane::simple_list::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:13: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame.hpp: In function ‘void takane::data_frame::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:14: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame_factor.hpp: In function ‘void takane::data_frame_factor::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:16: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/genomic_ranges.hpp: In function ‘void takane::genomic_ranges::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:21: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/compressed_sparse_matrix.hpp: In function ‘void takane::compressed_sparse_matrix::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:22: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘void takane::summarized_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘size_t takane::summarized_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:23: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/ranged_summarized_experiment.hpp: In function ‘void takane::ranged_summarized_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:24: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/single_cell_experiment.hpp: In function ‘void takane::single_cell_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:25: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/spatial_experiment.hpp: In function ‘void takane::spatial_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:26: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/multi_sample_dataset.hpp: In function ‘void takane::multi_sample_dataset::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:27: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp: In function ‘void takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 { | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 | }); | ~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:28: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bam_file.hpp: In function ‘void takane::bam_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:29: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bcf_file.hpp: In function ‘void takane::bcf_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:30: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigwig_file.hpp: In function ‘void takane::bigwig_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:31: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigbed_file.hpp: In function ‘void takane::bigbed_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:32: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fasta_file.hpp: In function ‘void takane::fasta_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:33: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp: In function ‘void takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 { | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:34: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bed_file.hpp: In function ‘void takane::bed_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:35: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gmt_file.hpp: In function ‘void takane::gmt_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:36: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp: In function ‘void takane::gff_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:37: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/rds_file.hpp: In function ‘void takane::rds_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:40: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘void takane::vcf_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘size_t takane::vcf_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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&)’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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"); | ^~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/uzuki2.hpp:17, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:8: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:578:28: required from here 578 | parse<DummyProvisioner>(reader, std::move(ext), std::move(options)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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); | ^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/validate.hpp:13, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/chihaya.hpp:10, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/utils_public.hpp:13, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:9: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/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]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/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-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)