############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Cardinal_2.10.0.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Cardinal_2.10.0.zip && rm Cardinal_2.10.0.tar.gz Cardinal_2.10.0.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 1092k 100 1092k 0 0 1593k 0 --:--:-- --:--:-- --:--:-- 1595k install for i386 * installing *source* package 'Cardinal' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DIP.cpp -o DIP.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynAlign.cpp -o dynAlign.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imzML.cpp -o imzML.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pugixml.cpp -o pugixml.o pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function] PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length) ^~~~~~~~~~~ pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function] PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length) ^~~~~~~~~~~~~ pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function] PUGI__FN size_t strlength_wide(const wchar_t* s) ^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c spatial.cpp -o spatial.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.o -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/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Cardinal' finding HTML links ... done AnnotatedImage-class html finding level-2 HTML links ... done AnnotatedImagingExperiment-class html Cardinal-package html ImageList-class html ImagingExperiment-class html ImagingResult-class html MSContinuousImagingExperiment-class html MSImagingExperiment-class html MSImagingInfo-class html MSProcessedImagingExperiment-class html MassDataFrame-class html PCA-methods html PLS-methods html PositionDataFrame-class html SparseImagingExperiment-class html XDataFrame-class html aggregate-methods html colocalized-methods html colors-functions html crossValidate-methods html defunct html deprecated html findNeighbors-methods html image-methods html internal html legacy html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/help/ImageData.html meansTest-methods html mz-methods html mzAlign-methods html mzBin-methods html mzFilter-methods html normalize-methods html peakAlign-methods html peakBin-methods html peakPick-methods html pixelApply-methods html plot-methods html process-methods html readMSIData html reduceBaseline-methods html reexports html selectROI-methods html simulateSpectrum html slice-methods html smoothSignal-methods html spatialDGMM-methods html spatialFastmap-methods html spatialKMeans-methods html spatialShrunkenCentroids-methods html subset-methods html topFeatures-methods html writeMSIData 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 'Cardinal' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DIP.cpp -o DIP.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynAlign.cpp -o dynAlign.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imzML.cpp -o imzML.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pugixml.cpp -o pugixml.o pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function] PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length) ^~~~~~~~~~~ pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function] PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length) ^~~~~~~~~~~~~ pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function] PUGI__FN size_t strlength_wide(const wchar_t* s) ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c spatial.cpp -o spatial.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.o -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/Cardinal.buildbin-libdir/Cardinal/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Cardinal' as Cardinal_2.10.0.zip * DONE (Cardinal) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'Cardinal' successfully unpacked and MD5 sums checked