############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/switchBox_1.30.0.tar.gz && rm -rf switchBox.buildbin-libdir && mkdir switchBox.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=switchBox.buildbin-libdir switchBox_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL switchBox_1.30.0.zip && rm switchBox_1.30.0.tar.gz switchBox_1.30.0.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 47 461k 47 219k 0 0 531k 0 --:--:-- --:--:-- --:--:-- 531k 100 461k 100 461k 0 0 685k 0 --:--:-- --:--:-- --:--:-- 685k install for i386 * installing *source* package 'switchBox' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o CalculateSignedScoreCore.cc: In function 'void CalculateSignedScoreCore(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*)': CalculateSignedScoreCore.cc:36:26: warning: variable 'pairsNo' set but not used [-Wunused-but-set-variable] int i,j,l,countplace,pairsNo; ^~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreCoreTieHandler.cc: In function 'void CalculateSignedScoreCoreTieHandler(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*)': CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable 'score1' [-Wunused-variable] double score1, score2, type; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCore.cc: In function 'void CalculateSignedScoreRestrictedPairsCore(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*)': CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable 'countplace' set but not used [-Wunused-but-set-variable] int i,l,countplace,pairsNo; ^~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o CalculateSignedScoreRestrictedPairsCoreTieHandler.cc: In function 'void CalculateSignedScoreRestrictedPairsCoreTieHandler(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)': CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable 'countplace' [-Wunused-variable] int i,l,countplace,pairsNo; ^~~~~~~~~~ CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable 'score1' [-Wunused-variable] double score1, score2, type; ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rinit.c -o rinit.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vect2compC.cc -o vect2compC.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o switchBox.dll tmp.def CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -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/switchBox.buildbin-libdir/00LOCK-switchBox/00new/switchBox/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'switchBox' finding HTML links ... done KTSP.Classify html KTSP.Train html SWAP.Calculate.BasicTSPScores html SWAP.Calculate.SignedTSPScores html SWAP.CalculateScores html SWAP.CalculateSignedScore html SWAP.Filter.Wilcoxon html SWAP.GetKTSP.PredictionStats html SWAP.GetKTSP.Result html SWAP.GetKTSP.TrainTestResults html SWAP.KTSP.CV html SWAP.KTSP.Classify html SWAP.KTSP.LOO html SWAP.KTSP.Statistic html SWAP.KTSP.Train html SWAP.Kby.Measurement html SWAP.Kby.Ttest html SWAP.MakeTSPTable html SWAP.PlotKTSP.GenePairBoxplot html SWAP.PlotKTSP.GenePairClassesBoxplot html SWAP.PlotKTSP.GenePairScatter html SWAP.PlotKTSP.Genes html SWAP.PlotKTSP.TrainTestROC html finding level-2 HTML links ... done Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpwX9sl3/R.INSTALL82874e1479b/switchBox/man/SWAP.PlotKTSP.TrainTestROC.Rd:35: missing link 'SWAP.GetkTSPTrainTestResults' SWAP.PlotKTSP.Votes html SWAP.Train.1TSP html SWAP.Train.KTSP html matTesting html matTraining html switchBox-package html testingGroup html trainingGroup 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 'switchBox' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o CalculateSignedScoreCore.cc: In function 'void CalculateSignedScoreCore(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*)': CalculateSignedScoreCore.cc:36:26: warning: variable 'pairsNo' set but not used [-Wunused-but-set-variable] int i,j,l,countplace,pairsNo; ^~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreCoreTieHandler.cc: In function 'void CalculateSignedScoreCoreTieHandler(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*)': CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable 'score1' [-Wunused-variable] double score1, score2, type; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCore.cc: In function 'void CalculateSignedScoreRestrictedPairsCore(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*)': CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable 'countplace' set but not used [-Wunused-but-set-variable] int i,l,countplace,pairsNo; ^~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o CalculateSignedScoreRestrictedPairsCoreTieHandler.cc: In function 'void CalculateSignedScoreRestrictedPairsCoreTieHandler(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)': CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable 'countplace' [-Wunused-variable] int i,l,countplace,pairsNo; ^~~~~~~~~~ CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable 'score1' [-Wunused-variable] double score1, score2, type; ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rinit.c -o rinit.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vect2compC.cc -o vect2compC.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o switchBox.dll tmp.def CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -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/switchBox.buildbin-libdir/switchBox/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'switchBox' as switchBox_1.30.0.zip * DONE (switchBox) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'switchBox' successfully unpacked and MD5 sums checked