############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BiocParallel_1.26.2.tar.gz && rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocParallel.buildbin-libdir BiocParallel_1.26.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BiocParallel_1.26.2.zip && rm BiocParallel_1.26.2.tar.gz BiocParallel_1.26.2.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 119k 100 119k 0 0 632k 0 --:--:-- --:--:-- --:--:-- 634k install for i386 * installing *source* package 'BiocParallel' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ipcmutex.cpp -o ipcmutex.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/fold.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/remove.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function_types/components.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17, from ipcmutex.cpp:3: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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/managed_shared_memory.hpp:27, from ipcmutex.cpp:13: 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:/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:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocParallel.buildbin-libdir/00LOCK-BiocParallel/00new/BiocParallel/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BiocParallel' finding HTML links ... done BatchJobsParam-class html BatchtoolsParam-class html BiocParallel-package html BiocParallelParam-class html DeveloperInterface html DoparParam-class html MulticoreParam-class html SerialParam-class html SnowParam-class html bpaggregate html bpiterate html bplapply html bploop html bpmapply html bpok html bpschedule html bptry html bpvalidate html bpvec html bpvectorize html ipcmutex html register 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 'BiocParallel' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ipcmutex.cpp -o ipcmutex.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/fold.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/remove.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function_types/components.hpp:44, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17, from ipcmutex.cpp:3: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ 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/managed_shared_memory.hpp:27, from ipcmutex.cpp:13: 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 '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:/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:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocParallel.buildbin-libdir/BiocParallel/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BiocParallel' as BiocParallel_1.26.2.zip * DONE (BiocParallel) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'BiocParallel' successfully unpacked and MD5 sums checked