############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ncdfFlow_2.38.0.tar.gz && rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ncdfFlow.buildbin-libdir ncdfFlow_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.38.0.zip && rm ncdfFlow_2.38.0.tar.gz ncdfFlow_2.38.0.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 55311 100 55311 0 0 326k 0 --:--:-- --:--:-- --:--:-- 327k install for i386 * installing *source* package 'ncdfFlow' ... ** using staged installation ** 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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bitOps.cpp -o bitOps.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hdfFlow.cpp -o hdfFlow.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/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/lexical_cast.hpp:30, from hdfFlow.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_::************ ^ hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector, unsigned int, unsigned int, double*, bool)': hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] herr_t status; ^~~~~~ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o 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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readFrame.cpp -o readFrame.o readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)': readFrame.cpp:98:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for(unsigned i = 0; i < j_val.size(); i++){ ~~^~~~~~~~~~~~~~ mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386" "C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386/libncdfFlow.a C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -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/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ncdfFlow' finding HTML links ... done Indices html as.flowSet html clone.ncdfFlowSet html extractFlowFrame html finding level-2 HTML links ... done flowSet-accessor html getFileName html lapply-methods html ncdfFlow html ncdfFlowList-class html ncdfFlowSet-Subset html ncdfFlowSet-class html ncdfFlowSet-constructor html ncdfFlowSet-split html ncfsApply-ncdfFlowSet-method html rbind2-method html read.ncdfFlowSet html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/help/read.ncdfFlowset.html replacement-method-for-ncdfFlowSet html save_ncfs html subset-functions html subset-methods html unlink-ncdfFlowSet-method 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 'ncdfFlow' ... ** 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/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bitOps.cpp -o bitOps.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hdfFlow.cpp -o hdfFlow.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/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/lexical_cast.hpp:30, from hdfFlow.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_::************ ^ hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector, unsigned int, unsigned int, double*, bool)': hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] herr_t status; ^~~~~~ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o 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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readFrame.cpp -o readFrame.o mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64" "C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -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/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ncdfFlow' as ncdfFlow_2.38.0.zip * DONE (ncdfFlow) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'ncdfFlow' successfully unpacked and MD5 sums checked