############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf tofsims.buildbin-libdir && mkdir tofsims.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tofsims.buildbin-libdir tofsims_1.20.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'tofsims' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LapackEigen.cpp -o LapackEigen.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:/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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c_importer.cpp -o c_importer.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nn.cpp -o nn.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readRawPhi.cpp -o readRawPhi.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utilities.cpp -o utilities.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o tofsims.dll tmp.def LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o utilities.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -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/tofsims.buildbin-libdir/00LOCK-tofsims/00new/tofsims/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'tofsims' finding HTML links ... done EigenDecompose html LapackGenEigen html MAF html MCR html MNF html MassImage html MassSpectra html PCA-class html PCAnalysis html PeakList html PrComp html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/tofsims.buildbin-libdir/00LOCK-tofsims/00new/tofsims/help/prComp.html PrinComp html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/tofsims.buildbin-libdir/00LOCK-tofsims/00new/tofsims/help/prinComp.html RSS-MCR-method html RSS html SNR html addFixedWidth html addPeaks html analysis html finding level-2 HTML links ... done analysisName html baseObject-PrComp-method html baseObject-PrinComp-method html baseObject html binning html bwApply html cReadRawPhi html calibPointNew html calibPoints html calibration html changePeakWidth html check.extension html computeMNF html computeNoise html coordToPixel-MassImage-numeric-method html coordToPixel html covDiffCalc html ctable html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/tofsims.buildbin-libdir/00LOCK-tofsims/00new/tofsims/help/cTable.html dim-MassImage-method html dim-MassSpectra-method html extract.header.data html findClosestMatch html findPeakWidth html getTOFs html image html imageMatrix html import html import.raw html instrument html iters-MCR-method html iters html itzipName-set html itzipName html legend.col html look.for.itzip.property html makeTIC-MassSpectra-method html makeTIC html manualSelectPeaks html mz html nComp html nPeaks html ndim-MassSpectra-method html ndim html nearestNeighbourMean html nnMNF html nnMean html noPlottingData-PCA-method html noPlottingData html nz html overlayPlot html parIndicesSearch html pcaLoadings html pcaMAF html pcaScores html peakIDs html peakMzs html peakPick html peakWidths html peaks2Spectra html plot-MassImage-missing-method html plot-PeakList-missing-method html plot html points html poissonScaling html readBIF html recalibrate html reduceSpectrumResolution html removePeaks html resids-MCR-method html resids html scale html show-MassImage-method html show-MassSpectra-method html show-PeakList-method html smoothScatter html smootherGolay html smootherSpline html subset html tofsims-package html unitMassPeaks html validMassImageObject html validMassSpectraObject html validPCAObject html validPeakListObject html xdim-MassImage-method html xdim-PCA-method html xdim-set html xdim html xy html xySpec html ydim-MassImage-method html ydim-PCA-method html ydim-set html ydim html zdim-MassSpectra-method html zdim 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 'tofsims' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LapackEigen.cpp -o LapackEigen.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:/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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c_importer.cpp -o c_importer.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nn.cpp -o nn.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readRawPhi.cpp -o readRawPhi.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utilities.cpp -o utilities.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o tofsims.dll tmp.def LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o utilities.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -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/tofsims.buildbin-libdir/tofsims/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'tofsims' as tofsims_1.20.0.zip * DONE (tofsims)