############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=MSstats.buildbin-libdir MSstats_4.3.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'MSstats' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c common.cpp -o common.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c comparison_contrasts.cpp -o comparison_contrasts.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c linear_summary.cpp -o linear_summary.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c median_polish.cpp -o median_polish.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o MSstats.dll tmp.def RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/meat/MSstats.buildbin-libdir/00LOCK-MSstats/00new/MSstats/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MSstats' finding HTML links ... done DDARawData html DDARawData.Skyline html DIARawData html DIAUmpiretoMSstatsFormat html MSstatsContrastMatrix html MSstatsGroupComparison html MSstatsGroupComparisonOutput html MSstatsGroupComparisonSingleProtein html MSstatsHandleMissing html MSstatsMergeFractions html MSstatsNormalize html MSstatsPrepareForDataProcess html MSstatsPrepareForGroupComparison html MSstatsPrepareForSummarization html MSstatsSelectFeatures html MSstatsSummarizationOutput html MSstatsSummarize html MSstatsSummarizeSingleLinear html MSstatsSummarizeSingleTMP html MaxQtoMSstatsFormat html OpenMStoMSstatsFormat html OpenSWATHtoMSstatsFormat html PDtoMSstatsFormat html ProgenesistoMSstatsFormat html SRMRawData html SkylinetoMSstatsFormat html SpectronauttoMSstatsFormat html checkRepeatedDesign html dataProcess html dataProcessPlots html designSampleSize html designSampleSizePlots html dot-addCoverageInfo html dot-addModelInformation html dot-addModelVariances html dot-addNInformativeInfo html dot-addNoisyFlag html dot-addOutlierCutoff html dot-addOutlierInformation html dot-addSurvivalPredictions html dot-adjustLRuns html dot-calculateOutlierCutoff html dot-calculatePower html dot-calculateProteinVariance html dot-checkContrastMatrix html dot-checkDataProcessParams html dot-checkExperimentDesign html dot-checkGCPlotsInput html dot-checkGroupComparisonInput html dot-checkSingleFeature html dot-checkSingleLabelProteins html dot-checkSingleSubject html dot-checkTechReplicate html dot-checkUnProcessedDataValidity html dot-countInformative html dot-countMissingPercentage html dot-documentFunction html dot-finalizeInput html dot-finalizeLinear html dot-finalizeTMP html dot-fitHuber html dot-fitLinearModel html dot-fitModelForGroupComparison html dot-fitModelSingleProtein html dot-fitTukey html dot-flagLowCoverage html dot-flagUninformativeSingleLabel html dot-getAllComparisons html dot-getContrast html dot-getContrastLabels html dot-getEmptyComparison html dot-getFeatureVariances html dot-getMedian html dot-getMedianSigmaSubject html dot-getMin html dot-getModelParameters html dot-getNonMissingFilter html dot-getNonMissingFilterStats html dot-getNumSample html dot-getSingleProteinForProfile html dot-getVarComponent html dot-getWideTable html dot-getYaxis html dot-handleEmptyConditions html dot-handleSingleContrast html dot-isSummarizable html dot-logDatasetInformation html dot-logMissingness html dot-logSingleLabeledProteins html dot-logSummaryStatistics html dot-makeComparison html dot-makeConditionPlot html dot-makeFactorColumns html dot-makeHeatmap html dot-makeProfilePlot html dot-makeQCPlot html dot-makeSummaryProfilePlot html dot-makeVolcano html dot-nicePrint html dot-normalizeGlobalStandards html dot-normalizeMedian html dot-normalizeQuantile html dot-onLoad html dot-plotComparison html dot-plotHeatmap html dot-plotVolcano html dot-preProcessIntensities html dot-prepareForDataProcess html dot-prepareLinear html dot-prepareSingleProteinForGC html dot-prepareSummary html dot-prepareTMP html dot-quantileNormalizationSingleLabel html dot-replaceZerosWithNA html dot-runTukey html dot-saveSessionInfo html dot-saveTable html dot-selectHighQualityFeatures html dot-selectTopFeatures html dot-setCensoredByThreshold html dot-updateColumnsForProcessing html dot-updateUnequalVariances html getProcessed html getSamplesInfo html getSelectedProteins html groupComparison html groupComparisonPlots html makePeptidesDictionary html modelBasedQCPlots html quantification html savePlot html theme_msstats 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 * MD5 sums packaged installation of 'MSstats' as MSstats_4.3.0.zip * DONE (MSstats)