############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘alabaster.base’ ... ** this is package ‘alabaster.base’ version ‘1.7.8’ ** 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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c check_list.cpp -o check_list.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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c load_list.cpp -o load_list.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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c validate.cpp -o validate.o In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:12, from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/takane.hpp:4, from validate.cpp:2: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/assorthead/include/takane/simple_list.hpp:145:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 145 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list"); | ^~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/simple_list.hpp:145:76: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"simple_list"), std::allocator()))’ 145 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:22: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:124:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 124 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ^~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:124:54: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"summarized_experiment"), std::allocator()))’ 124 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘std::vector takane::summarized_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:137:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 137 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ^~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:137:54: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"summarized_experiment"), std::allocator()))’ 137 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:27: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/assorthead/include/takane/sequence_string_set.hpp:366:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 366 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set"); | ^~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/sequence_string_set.hpp:366:72: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"sequence_string_set"), std::allocator()))’ 366 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:40: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:241:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 241 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ^~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:241:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"vcf_experiment"), std::allocator()))’ 241 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘std::vector takane::vcf_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’: /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:253:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] 253 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ^~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:253:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string(((const char*)"vcf_experiment"), std::allocator()))’ 253 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/validate.hpp:13, from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/chihaya.hpp:10, from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/utils_public.hpp:13, from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:9: /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = int]’: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = long unsigned int]’: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c vls.cpp -o vls.o /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 vls.o /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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)