############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pqsfinder_2.10.1.tar.gz && rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pqsfinder.buildbin-libdir pqsfinder_2.10.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pqsfinder_2.10.1.zip && rm pqsfinder_2.10.1.tar.gz pqsfinder_2.10.1.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 88479 100 88479 0 0 152k 0 --:--:-- --:--:-- --:--:-- 152k 100 88479 100 88479 0 0 152k 0 --:--:-- --:--:-- --:--:-- 152k install for i386 * installing *source* package 'pqsfinder' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pqsfinder.cpp -o pqsfinder.o pqsfinder.cpp: In function 'void find_all_runs(SEXP, int, std::__cxx11::basic_string::const_iterator, std::__cxx11::basic_string::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)': pqsfinder.cpp:584:53: warning: 'loop_len' may be used uninitialized in this function [-Wmaybe-uninitialized] pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop), ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex.cpp -o boost_regex/regex.o mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386" "C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386/libboost_regex.a" boost_regex/static_mutex.o boost_regex/regex_debug.o boost_regex/wide_posix_api.o boost_regex/posix_api.o boost_regex/regex.o C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386/libboost_regex.a C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o pqsfinder.dll tmp.def RcppExports.o pqsfinder.o C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/i386/libboost_regex.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'pqsfinder' finding HTML links ... done PQSViews-class html finding level-2 HTML links ... done PQSViews html as.character-PQSViews-method html density-PQSViews-method html maxScores-PQSViews-method html maxScores html pqsfinder html score-PQSViews-method html show-PQSViews-method html strand-PQSViews-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 'pqsfinder' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pqsfinder.cpp -o pqsfinder.o pqsfinder.cpp: In function 'void find_all_runs(SEXP, int, std::__cxx11::basic_string::const_iterator, std::__cxx11::basic_string::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)': pqsfinder.cpp:584:53: warning: 'loop_len' may be used uninitialized in this function [-Wmaybe-uninitialized] pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop), ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_regex/regex.cpp -o boost_regex/regex.o mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64" "C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a" boost_regex/static_mutex.o boost_regex/regex_debug.o boost_regex/wide_posix_api.o boost_regex/posix_api.o boost_regex/regex.o C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o pqsfinder.dll tmp.def RcppExports.o pqsfinder.o C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'pqsfinder' as pqsfinder_2.10.1.zip * DONE (pqsfinder) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'pqsfinder' successfully unpacked and MD5 sums checked