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This page was generated on 2021-10-15 15:06:13 -0400 (Fri, 15 Oct 2021).

INSTALL results for MSstats on tokay2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstats.git to
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raw results

Package 1208/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 4.0.1  (landing page)
Meena Choi
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MSstats
git_branch: RELEASE_3_13
git_last_commit: afa9e58
git_last_commit_date: 2021-05-31 23:11:01 -0400 (Mon, 31 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstats
Version: 4.0.1
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSstats_4.0.1.tar.gz && rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstats.buildbin-libdir MSstats_4.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSstats_4.0.1.zip && rm MSstats_4.0.1.tar.gz MSstats_4.0.1.zip
StartedAt: 2021-10-14 08:28:55 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 08:30:53 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 118.3 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSstats_4.0.1.tar.gz && rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstats.buildbin-libdir MSstats_4.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSstats_4.0.1.zip && rm MSstats_4.0.1.tar.gz MSstats_4.0.1.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'MSstats' ...
** 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"  -fopenmp   -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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c common.cpp -o common.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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c comparison_contrasts.cpp -o comparison_contrasts.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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c linear_summary.cpp -o linear_summary.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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c median_polish.cpp -o median_polish.o
C:/rtools40/mingw32/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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/MSstats.buildbin-libdir/00LOCK-MSstats/00new/MSstats/libs/i386
** 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

install for x64

* installing *source* package 'MSstats' ...
** 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"  -fopenmp   -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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c common.cpp -o common.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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c comparison_contrasts.cpp -o comparison_contrasts.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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c linear_summary.cpp -o linear_summary.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"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/MSstats.buildbin-libdir/MSstats/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstats' as MSstats_4.0.1.zip
* DONE (MSstats)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MSstats' successfully unpacked and MD5 sums checked