############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/slalom_1.16.0.tar.gz && rm -rf slalom.buildbin-libdir && mkdir slalom.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=slalom.buildbin-libdir slalom_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL slalom_1.16.0.zip && rm slalom_1.16.0.tar.gz slalom_1.16.0.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 2 17.1M 2 421k 0 0 588k 0 0:00:29 --:--:-- 0:00:29 588k 9 17.1M 9 1745k 0 0 1034k 0 0:00:16 0:00:01 0:00:15 1035k 22 17.1M 22 4022k 0 0 1495k 0 0:00:11 0:00:02 0:00:09 1495k 41 17.1M 41 7246k 0 0 1959k 0 0:00:08 0:00:03 0:00:05 1959k 64 17.1M 64 10.9M 0 0 2390k 0 0:00:07 0:00:04 0:00:03 2390k 90 17.1M 90 15.5M 0 0 2798k 0 0:00:06 0:00:05 0:00:01 3115k 100 17.1M 100 17.1M 0 0 2946k 0 0:00:05 0:00:05 --:--:-- 3700k install for i386 * installing *source* package 'slalom' ... ** 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/RcppArmadillo/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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c slalom-classes.cpp -o slalom-classes.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/lexical_cast.hpp:30, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20, from slalom-classes.cpp:20: C:/Users/biocbuild/bbs-3.14-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-3.14-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_::************ ^ slalom-classes.cpp: In member function 'void SlalomModel::train()': slalom-classes.cpp:223:20: warning: unused variable 'meanerr' [-Wunused-variable] double meanerr = arma::mean(error); ^~~~~~~ slalom-classes.cpp:202:12: warning: unused variable 'meanerr' [-Wunused-variable] double meanerr = arma::mean(error); ^~~~~~~ slalom-classes.cpp: In member function 'void SlalomModel::updateEpsilon()': slalom-classes.cpp:431:23: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < this->epsilon_E1.n_elem; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o slalom.dll tmp.def RcppExports.o slalom-classes.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/slalom.buildbin-libdir/00LOCK-slalom/00new/slalom/libs/i386 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'slalom' finding HTML links ... done Rcpp_SlalomModel html SlalomModel html addResultsToSingleCellExperiment html initSlalom html mesc html newSlalomModel html plotLoadings html plotRelevance html plotTerms html slalom html topTerms html trainSlalom html updateSlalom 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 'slalom' ... ** 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/RcppArmadillo/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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c slalom-classes.cpp -o slalom-classes.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/lexical_cast.hpp:30, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20, from slalom-classes.cpp:20: C:/Users/biocbuild/bbs-3.14-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-3.14-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_::************ ^ slalom-classes.cpp: In member function 'void SlalomModel::train()': slalom-classes.cpp:223:20: warning: unused variable 'meanerr' [-Wunused-variable] double meanerr = arma::mean(error); ^~~~~~~ slalom-classes.cpp:202:12: warning: unused variable 'meanerr' [-Wunused-variable] double meanerr = arma::mean(error); ^~~~~~~ slalom-classes.cpp: In member function 'void SlalomModel::updateEpsilon()': slalom-classes.cpp:431:23: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < this->epsilon_E1.n_elem; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o slalom.dll tmp.def RcppExports.o slalom-classes.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/slalom.buildbin-libdir/slalom/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'slalom' as slalom_1.16.0.zip * DONE (slalom) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'slalom' successfully unpacked and MD5 sums checked