############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSnbase_2.18.0.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSnbase_2.18.0.zip && rm MSnbase_2.18.0.tar.gz MSnbase_2.18.0.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 1789k 100 1789k 0 0 1911k 0 --:--:-- --:--:-- --:--:-- 1913k install for i386 * installing *source* package 'MSnbase' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function] static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, ^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function] static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, ^~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o "C:/rtools40/mingw32/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function 'compar_double_dd_for_stable_asc_order': utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^~~ utils.c: In function 'compar_double_dd_for_stable_desc_order': utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^~~ utils.c: In function 'compar_double_asc_order': utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^~~ utils.c: In function 'compar_double_desc_order': utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^~~ At top level: utils.c:131:12: warning: 'compar_double_desc_order' defined but not used [-Wunused-function] static int compar_double_desc_order(const void *p1, const void *p2) ^~~~~~~~~~~~~~~~~~~~~~~~ utils.c:121:12: warning: 'compar_double_asc_order' defined but not used [-Wunused-function] static int compar_double_asc_order(const void *p1, const void *p2) ^~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.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/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/libs/i386 ** R ** data *** moving datasets to lazyload DB Creating a new generic function for 'trimws' in package 'MSnbase' in method for 'coerce' with signature '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment" in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment" in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra" ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'trimws' in package 'MSnbase' in method for 'coerce' with signature '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment" in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment" in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra" ** help *** installing help indices converting help for package 'MSnbase' finding HTML links ... done Chromatogram-class html finding level-2 HTML links ... done FeatComp-class html FeaturesOfInterest-class html MChromatograms-class html MIAPE-class html MSmap-class html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/help/msMap.html MSnExp-class html MSnProcess-class html MSnSet-class html MSnSetList-class html MSnbaseOptions html MSpectra html MzTab-class html OnDiskMSnExp-class html ProcessingStep-class html ReporterIons-class html Spectrum-class html Spectrum1-class html Spectrum2-class html TMT6 html addIdentificationData-methods html aggvar html averageMSnSet html bin-methods html calculateFragments-methods html chromatogram-MSnExp-method html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/help/chromatogram.html clean-methods html combineFeatures html combineSpectra html combineSpectraMovingWindow html commonFeatureNames html compareMSnSets html compareSpectra-methods html consensusSpectrum html defunct html estimateMzResolution html estimateMzScattering html estimateNoise-method html extractPrecSpectra-methods html extractSpectraData html fData-utils html factorsAsStrings html featureCV html fillUp html filterIdentificationDataFrame html formatRt html get.amino.acids html get.atomic.mass html getVariableName html grepEcols html hasSpectraOrChromatograms html iPQF html iTRAQ4 html imageNA2 html impute html isCentroidedFromFile html itraqdata html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/help/msnset.html listOf html makeCamelCase html makeNaData html meanMzInts html missing-data html mzRident2dfr html nFeatures html nQuants html naplot html navMS html normToReference html normalise-methods html npcv html pSet-class html pickPeaks-method html plot-methods html plot2d-methods html plotDensity-methods html plotMzDelta-methods html plotNA-methods html plotSpectrumSpectrum-methods html precSelection html purityCorrect-methods html quantify-methods html readMSData html readMSnSet html readMgfData html readMzIdData html readMzTabData html readMzTabData_v0.9 html readSRMData html reduce-data.frame-method html removeNoId-methods html removePeaks-methods html removeReporters-methods html selectFeatureData html smooth-methods html trimMz-methods html updateObject-methods html writeMSData html writeMgfData-methods html writeMzTabData 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 'MSnbase' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function] static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function] static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, ^~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o "C:/rtools40/mingw64/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function 'compar_double_dd_for_stable_asc_order': utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^~~ utils.c: In function 'compar_double_dd_for_stable_desc_order': utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^~~ utils.c: In function 'compar_double_asc_order': utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^~~ utils.c: In function 'compar_double_desc_order': utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^~~ At top level: utils.c:131:12: warning: 'compar_double_desc_order' defined but not used [-Wunused-function] static int compar_double_desc_order(const void *p1, const void *p2) ^~~~~~~~~~~~~~~~~~~~~~~~ utils.c:121:12: warning: 'compar_double_asc_order' defined but not used [-Wunused-function] static int compar_double_asc_order(const void *p1, const void *p2) ^~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.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/MSnbase.buildbin-libdir/MSnbase/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'MSnbase' as MSnbase_2.18.0.zip * DONE (MSnbase) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'MSnbase' successfully unpacked and MD5 sums checked