############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GOpro_1.18.0.tar.gz && rm -rf GOpro.buildbin-libdir && mkdir GOpro.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOpro.buildbin-libdir GOpro_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GOpro_1.18.0.zip && rm GOpro_1.18.0.tar.gz GOpro_1.18.0.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 10 737k 10 76827 0 0 370k 0 0:00:01 --:--:-- 0:00:01 369k 100 737k 100 737k 0 0 1017k 0 --:--:-- --:--:-- --:--:-- 1017k install for i386 * installing *source* package 'GOpro' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GOpro_init.c -o GOpro_init.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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fisher.cpp -o fisher.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_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/error_handling.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/detail/common_error_handling.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/hypergeometric.hpp:12, from fisher.cpp:2: 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/math/constants/constants.hpp:11, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/detail/hypergeometric_pdf.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/hypergeometric.hpp:14, from fisher.cpp:2: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:99:88: note: #pragma message: CAUTION: One or more C++11 features were found to be unavailable BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/detail/hypergeometric_pdf.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/hypergeometric.hpp:14, from fisher.cpp:2: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:100:139: note: #pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021. BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:101:106: note: #pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message. BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:102:108: note: #pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_THREAD_LOCAL BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) ^ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GOpro.dll tmp.def GOpro_init.o RcppExports.o fisher.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/GOpro.buildbin-libdir/00LOCK-GOpro/00new/GOpro/libs/i386 ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GOpro' finding HTML links ... done GOpro html exrtcga html findGO 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 'GOpro' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GOpro_init.c -o GOpro_init.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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fisher.cpp -o fisher.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_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/error_handling.hpp:21, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/detail/common_error_handling.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/hypergeometric.hpp:12, from fisher.cpp:2: 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_::************ ^ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GOpro.dll tmp.def GOpro_init.o RcppExports.o fisher.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/GOpro.buildbin-libdir/GOpro/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'GOpro' as GOpro_1.18.0.zip * DONE (GOpro) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'GOpro' successfully unpacked and MD5 sums checked