############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'alabaster.base' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++17 g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_list.cpp -o check_list.o In file included from ../inst/include/uzuki2/uzuki2.hpp:14, from check_list.cpp:3: ../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of 'std::shared_ptr uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const std::string&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_hdf5.hpp:442:50: required from 'std::shared_ptr uzuki2::Hdf5Parser::parse(const H5::Group&, const std::string&, Externals) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals; std::string = std::__cxx11::basic_string]' ../inst/include/uzuki2/parse_hdf5.hpp:521:32: required from here ../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 227 | for (int i = 0; i < len; ++i) { | ~~^~~~~ ../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'long long unsigned int' [-Wsign-compare] 295 | if (x < 0 || x >= levlen) { | ~~^~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c load_csv.cpp -o load_csv.o load_csv.cpp: In instantiation of 'void RFilledField::add_missing() [with T = std::complex; comservatory::Type tt = comservatory::COMPLEX; RVector = Rcpp::Vector<15>]': load_csv.cpp:36:10: required from here load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 37 | if (position >= store.size()) { | ~~~~~~~~~^~~~~~~~~~~~~~~ load_csv.cpp: In instantiation of 'void RFilledField::add_missing() [with T = bool; comservatory::Type tt = comservatory::BOOLEAN; RVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]': load_csv.cpp:36:10: required from here load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] load_csv.cpp: In instantiation of 'void RFilledField::push_back(T) [with T = bool; comservatory::Type tt = comservatory::BOOLEAN; RVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]': load_csv.cpp:27:10: required from here load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 28 | if (position >= store.size()) { | ~~~~~~~~~^~~~~~~~~~~~~~~ load_csv.cpp: In instantiation of 'void RFilledField::add_missing() [with T = double; comservatory::Type tt = comservatory::NUMBER; RVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]': load_csv.cpp:36:10: required from here load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 37 | if (position >= store.size()) { | ~~~~~~~~~^~~~~~~~~~~~~~~ load_csv.cpp: In instantiation of 'void RFilledField::push_back(T) [with T = double; comservatory::Type tt = comservatory::NUMBER; RVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]': load_csv.cpp:27:10: required from here load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 28 | if (position >= store.size()) { | ~~~~~~~~~^~~~~~~~~~~~~~~ load_csv.cpp: In instantiation of 'void RFilledField::add_missing() [with T = std::__cxx11::basic_string; comservatory::Type tt = comservatory::STRING; RVector = Rcpp::Vector<16>]': load_csv.cpp:36:10: required from here load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 37 | if (position >= store.size()) { | ~~~~~~~~~^~~~~~~~~~~~~~~ load_csv.cpp: In instantiation of 'void RFilledField::push_back(T) [with T = std::__cxx11::basic_string; comservatory::Type tt = comservatory::STRING; RVector = Rcpp::Vector<16>]': load_csv.cpp:27:10: required from here load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 28 | if (position >= store.size()) { | ~~~~~~~~~^~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c load_list.cpp -o load_list.o In file included from ../inst/include/uzuki2/uzuki2.hpp:14, from load_list.cpp:3: ../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of 'std::shared_ptr uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const std::string&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_hdf5.hpp:442:50: required from 'std::shared_ptr uzuki2::Hdf5Parser::parse(const H5::Group&, const std::string&, Externals) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals; std::string = std::__cxx11::basic_string]' ../inst/include/uzuki2/parse_hdf5.hpp:521:32: required from here ../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 227 | for (int i = 0; i < len; ++i) { | ~~^~~~~ ../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'long long unsigned int' [-Wsign-compare] 295 | if (x < 0 || x >= levlen) { | ~~^~~~~~~~~ ../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of 'std::shared_ptr uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const std::string&) [with Provisioner = RProvisioner; Externals = uzuki2::ExternalTracker; std::string = std::__cxx11::basic_string]': ../inst/include/uzuki2/parse_hdf5.hpp:442:50: required from 'std::shared_ptr uzuki2::Hdf5Parser::parse(const H5::Group&, const std::string&, Externals) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string]' ../inst/include/uzuki2/parse_hdf5.hpp:486:34: required from 'std::shared_ptr uzuki2::Hdf5Parser::parse(const std::string&, const std::string&, Externals) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string]' load_list.cpp:288:56: required from here ../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 227 | for (int i = 0; i < len; ++i) { | ~~^~~~~ ../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'long long unsigned int' [-Wsign-compare] 295 | if (x < 0 || x >= levlen) { | ~~^~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_scalar.cpp -o write_scalar.o g++ -shared -s -static-libgcc -o alabaster.base.dll tmp.def RcppExports.o check_csv.o check_list.o load_csv.o load_list.o write_scalar.o -LF:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lz -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/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 * DONE (alabaster.base)