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INSTALL report for pRoloc on tokay1

This page was generated on 2020-04-15 12:21:11 -0400 (Wed, 15 Apr 2020).

Package 1313/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRoloc 1.26.0
Laurent Gatto
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/pRoloc
Branch: RELEASE_3_10
Last Commit: c5fe2c7
Last Changed Date: 2019-10-29 13:08:35 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  ERROR  OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: pRoloc
Version: 1.26.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/pRoloc_1.26.0.tar.gz && rm -rf pRoloc.buildbin-libdir && mkdir pRoloc.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pRoloc.buildbin-libdir pRoloc_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL pRoloc_1.26.0.zip && rm pRoloc_1.26.0.tar.gz pRoloc_1.26.0.zip
StartedAt: 2020-04-14 20:38:30 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 20:40:40 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 130.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/pRoloc_1.26.0.tar.gz && rm -rf pRoloc.buildbin-libdir && mkdir pRoloc.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pRoloc.buildbin-libdir pRoloc_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL pRoloc_1.26.0.zip && rm pRoloc_1.26.0.tar.gz pRoloc_1.26.0.zip
###
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install for i386

* installing *source* package 'pRoloc' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c dmvtCpp.cpp -o dmvtCpp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c pRoloc.cpp -o pRoloc.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/pRoloc.buildbin-libdir/00LOCK-pRoloc/00new/pRoloc/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'BiocGenerics::type' by 'kernlab::type' when loading 'pRoloc'
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'pRoloc'
** help
*** installing help indices
  converting help for package 'pRoloc'
    finding HTML links ... done
    AnnotationParams-class                  html  
    ClustDist-class                         html  
    ClustDistList-class                     html  
    GenRegRes-class                         html  
    finding level-2 HTML links ... done

    MCMCParams                              html  
    MLearn-methods                          html  
    MartInstance-class                      html  
    QSep-class                              html  
    SpatProtVis-class                       html  
    addGoAnnotations                        html  
    addLegend                               html  
    addMarkers                              html  
    checkFeatureNamesOverlap                html  
    checkFvarOverlap                        html  
    chi2-methods                            html  
    classWeights                            html  
    clustDist                               html  
    defunct                                 html  
    empPvalues                              html  
    exprsToRatios-methods                   html  
    fDataToUnknown                          html  
    filterBinMSnSet                         html  
    filterMaxMarkers                        html  
    filterMinMarkers                        html  
    filterZeroCols                          html  
    getGOFromFeatures                       html  
    getMarkerClasses                        html  
    getMarkers                              html  
    getNormDist                             html  
    getPredictions                          html  
    getStockcol                             html  
    goIdToTerm                              html  
    highlightOnPlot                         html  
    knnClassification                       html  
    knnOptimisation                         html  
    knntlClassification                     html  
    knntlOptimisation                       html  
    ksvmClassification                      html  
    ksvmOptimisation                        html  
    lopims                                  html  
    makeGoSet                               html  
    markerMSnSet                            html  
    markers                                 html  
    mcmc-helpers                            html  
    minMarkers                              html  
    move2Ds                                 html  
    mrkConsProfiles                         html  
    mrkHClust                               html  
    nbClassification                        html  
    nbOptimisation                          html  
    nndist-methods                          html  
    nnetClassification                      html  
    nnetOptimisation                        html  
    orderGoAnnotations                      html  
    orgQuants                               html  
    pRolocmarkers                           html  
    perTurboClassification                  html  
    perTurboOptimisation                    html  
    phenoDisco                              html  
    plot2D                                  html  
    plot2Ds                                 html  
    plotConsProfiles                        html  
    plotDist                                html  
    plotEllipse                             html  
    plsdaClassification                     html  
    plsdaOptimisation                       html  
    rfClassification                        html  
    rfOptimisation                          html  
    sampleMSnSet                            html  
    showGOEvidenceCodes                     html  
    subsetMarkers                           html  
    svmClassification                       html  
    svmOptimisation                         html  
    tagm-map                                html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu4t8oq/R.INSTALL2bf03a75e97/pRoloc/man/tagm-map.Rd:27: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu4t8oq/R.INSTALL2bf03a75e97/pRoloc/man/tagm-map.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu4t8oq/R.INSTALL2bf03a75e97/pRoloc/man/tagm-map.Rd:79: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
    tagm-mcmc                               html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu4t8oq/R.INSTALL2bf03a75e97/pRoloc/man/tagm-mcmc.Rd:24: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu4t8oq/R.INSTALL2bf03a75e97/pRoloc/man/tagm-mcmc.Rd:115: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu4t8oq/R.INSTALL2bf03a75e97/pRoloc/man/tagm-mcmc.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
    testMSnSet                              html  
    testMarkers                             html  
    thetas                                  html  
    undocumented                            html  
    zerosInBinMSnSet                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'BiocGenerics::type' by 'kernlab::type' when loading 'pRoloc'
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'pRoloc'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'BiocGenerics::type' by 'kernlab::type' when loading 'pRoloc'
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'pRoloc'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'pRoloc' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c dmvtCpp.cpp -o dmvtCpp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c pRoloc.cpp -o pRoloc.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/pRoloc.buildbin-libdir/pRoloc/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::type' by 'kernlab::type' when loading 'pRoloc'
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'pRoloc'
* MD5 sums
packaged installation of 'pRoloc' as pRoloc_1.26.0.zip
* DONE (pRoloc)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'pRoloc' successfully unpacked and MD5 sums checked