############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SharedObject_1.6.0.tar.gz && rm -rf SharedObject.buildbin-libdir && mkdir SharedObject.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SharedObject.buildbin-libdir SharedObject_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SharedObject_1.6.0.zip && rm SharedObject_1.6.0.tar.gz SharedObject_1.6.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 83603 100 83603 0 0 530k 0 --:--:-- --:--:-- --:--:-- 533k install for i386 * installing *source* package 'SharedObject' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs mkdir -p ../inst/include&&\ mkdir -p ../inst/include/SharedObject&&\ mkdir -p ../inst/usrlib/i386 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c C_interface.cpp -o C_interface.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c altrep.cpp -o altrep.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c altrepRegistration.cpp -o altrepRegistration.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c numericAltrepOperations.cpp -o numericAltrepOperations.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sharedMemory.cpp -o sharedMemory.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/shm/named_semaphore.hpp:29, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/named_semaphore.hpp:37, from sharedMemory.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'boost::interprocess::ipcdetail::ref_count_ptr* boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::find(const char*)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp:405:43: warning: '.boost::container::dtl::basic_string_base >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized] { return this->members_.plong_repr()->start; } ^~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'boost::interprocess::ipcdetail::ref_count_ptr* boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::insert(const char*, const boost::interprocess::ipcdetail::ref_count_ptr&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp:405:43: warning: '.boost::container::dtl::basic_string_base >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized] { return this->members_.plong_repr()->start; } ^~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'bool boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::erase(const char*)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp:405:43: warning: '.boost::container::dtl::basic_string_base >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized] { return this->members_.plong_repr()->start; } ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sharedObjectClass.cpp -o sharedObjectClass.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stringAltrepOperations.cpp -o stringAltrepOperations.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o SharedObject.dll tmp.def C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR "C:/rtools40/mingw32/bin/"ar -crv SharedObject.a *.o a - C_interface.o a - RcppExports.o a - altrep.o a - altrepRegistration.o a - numericAltrepOperations.o a - sharedMemory.o a - sharedObjectClass.o a - stringAltrepOperations.o a - utils.o cp "sharedMemory.h" "../inst/include/SharedObject/"&&\ cp "SharedObject.a" "../inst/usrlib/i386/" installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SharedObject.buildbin-libdir/00LOCK-SharedObject/00new/SharedObject/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SharedObject' finding HTML links ... done SharedObject html developer-API html is.altrep html is.shared html listSharedObjects html pkgconfig html share html sharedObjectPkgOptions html sharedObjectProperties html unshare html ** 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 install for x64 * installing *source* package 'SharedObject' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs mkdir -p ../inst/include&&\ mkdir -p ../inst/include/SharedObject&&\ mkdir -p ../inst/usrlib/x64 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c C_interface.cpp -o C_interface.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c altrep.cpp -o altrep.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c altrepRegistration.cpp -o altrepRegistration.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c numericAltrepOperations.cpp -o numericAltrepOperations.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sharedMemory.cpp -o sharedMemory.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/shm/named_semaphore.hpp:29, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/named_semaphore.hpp:37, from sharedMemory.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'boost::interprocess::ipcdetail::ref_count_ptr* boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::find(const char*)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp:405:43: warning: '.boost::container::dtl::basic_string_base >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized] { return this->members_.plong_repr()->start; } ^~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'boost::interprocess::ipcdetail::ref_count_ptr* boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::insert(const char*, const boost::interprocess::ipcdetail::ref_count_ptr&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp:405:43: warning: '.boost::container::dtl::basic_string_base >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized] { return this->members_.plong_repr()->start; } ^~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'bool boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::erase(const char*)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/string.hpp:405:43: warning: '.boost::container::dtl::basic_string_base >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized] { return this->members_.plong_repr()->start; } ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sharedObjectClass.cpp -o sharedObjectClass.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stringAltrepOperations.cpp -o stringAltrepOperations.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o SharedObject.dll tmp.def C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR "C:/rtools40/mingw64/bin/"ar -crv SharedObject.a *.o a - C_interface.o a - RcppExports.o a - altrep.o a - altrepRegistration.o a - numericAltrepOperations.o a - sharedMemory.o a - sharedObjectClass.o a - stringAltrepOperations.o a - utils.o cp "sharedMemory.h" "../inst/include/SharedObject/"&&\ cp "SharedObject.a" "../inst/usrlib/x64/" installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SharedObject.buildbin-libdir/SharedObject/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SharedObject' as SharedObject_1.6.0.zip * DONE (SharedObject) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'SharedObject' successfully unpacked and MD5 sums checked