############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf alabaster.base.buildbin-libdir && mkdir alabaster.base.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=alabaster.base.buildbin-libdir alabaster.base_1.7.8.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'alabaster.base' ... ** this is package 'alabaster.base' version '1.7.8' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' using C++17 g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_csv.cpp -o check_csv.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_list.cpp -o check_list.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c is_rfc3339.cpp -o is_rfc3339.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c load_csv.cpp -o load_csv.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c load_list.cpp -o load_list.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c validate.cpp -o validate.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:12, from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/takane.hpp:4, from validate.cpp:2: E:/biocbuild/bbs-3.21-bioc/R/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&)': E:/biocbuild/bbs-3.21-bioc/R/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"); | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:22: E:/biocbuild/bbs-3.21-bioc/R/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&)': E:/biocbuild/bbs-3.21-bioc/R/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"); | ^~~~~ E:/biocbuild/bbs-3.21-bioc/R/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/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&)': E:/biocbuild/bbs-3.21-bioc/R/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"); | ^~~~~ E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:27: E:/biocbuild/bbs-3.21-bioc/R/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&)': E:/biocbuild/bbs-3.21-bioc/R/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"); | ^~~ E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:40: E:/biocbuild/bbs-3.21-bioc/R/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&)': E:/biocbuild/bbs-3.21-bioc/R/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"); | ^~~~~~ E:/biocbuild/bbs-3.21-bioc/R/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"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/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&)': E:/biocbuild/bbs-3.21-bioc/R/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"); | ^~~~~~ E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/validate.hpp:13, from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/chihaya.hpp:10, from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/utils_public.hpp:13, from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:9: E:/biocbuild/bbs-3.21-bioc/R/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]': E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: 'previous' may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: 'previous' was declared here 45 | Index_ previous; | ^~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/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 long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: 'previous' may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: 'previous' was declared here 45 | Index_ previous; | ^~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vls.cpp -o vls.o g++ -shared -s -static-libgcc -o alabaster.base.dll tmp.def 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 -LE:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lz -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/meat/alabaster.base.buildbin-libdir/00LOCK-alabaster.base/00new/alabaster.base/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'alabaster.base' as alabaster.base_1.7.8.zip * DONE (alabaster.base)