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surveillance log file (build_win64)

Wed Mar 27 15:40:31 2019: Building binary for package surveillance (SVN revision 2425)
using R version 3.5.3 Patched (2019-03-11 r76268) ...

* installing to library 'R:/lib/local/3.5'
* installing *source* package 'surveillance' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c backproj.cc -o backproj.o
c:/Rtools/mingw_32/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c determineSources.cc -o determineSources.o
c:/Rtools/mingw_32/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
c:/Rtools/mingw_32/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ks.c -o ks.o
c:/Rtools/mingw_32/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c stcd-assuncaocorrea.cc -o stcd-assuncaocorrea.o
c:/Rtools/mingw_32/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c surveillance.c -o surveillance.o
c:/Rtools/mingw_32/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c twins.cc -o twins.o
c:/Rtools/mingw_32/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c twinstim_siaf_polyCub_iso.c -o twinstim_siaf_polyCub_iso.o
c:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o surveillance.dll tmp.def RcppExports.o backproj.o determineSources.o init.o ks.o stcd-assuncaocorrea.o surveillance.o twins.o twinstim_siaf_polyCub_iso.o -LR:/base/local215/lib/i386 -LR:/base/local215/lib -LR:/lib/R/R-patched/bin/i386 -lR
installing to R:/lib/local/3.5/surveillance/libs/i386

*** arch - x64
c:/Rtools/mingw_64/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c backproj.cc -o backproj.o
c:/Rtools/mingw_64/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c determineSources.cc -o determineSources.o
c:/Rtools/mingw_64/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
c:/Rtools/mingw_64/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ks.c -o ks.o
c:/Rtools/mingw_64/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c stcd-assuncaocorrea.cc -o stcd-assuncaocorrea.o
c:/Rtools/mingw_64/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c surveillance.c -o surveillance.o
c:/Rtools/mingw_64/bin/g++  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -mtune=generic -c twins.cc -o twins.o
c:/Rtools/mingw_64/bin/gcc  -I"R:/lib/R/R-patched/include" -DNDEBUG  -I"R:/lib/local/3.5/Rcpp/include" -I"R:/lib/local/3.5/polyCub/include"   -I"R:/base/local215/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c twinstim_siaf_polyCub_iso.c -o twinstim_siaf_polyCub_iso.o
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o surveillance.dll tmp.def RcppExports.o backproj.o determineSources.o init.o ks.o stcd-assuncaocorrea.o surveillance.o twins.o twinstim_siaf_polyCub_iso.o -LR:/base/local215/lib/x64 -LR:/base/local215/lib -LR:/lib/R/R-patched/bin/x64 -lR
installing to R:/lib/local/3.5/surveillance/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'surveillance'
    finding HTML links ... done
    LRCUSUM.runlength                       html  
    MMRcoverageDE                           html  
    R0                                      html  
    abattoir                                html  
    addFormattedXAxis                       html  
    addSeason2formula                       html  
    aggregate.disProg                       html  
    algo.bayes                              html  
    algo.call                               html  
    algo.cdc                                html  
    algo.compare                            html  
    algo.cusum                              html  
    algo.farrington                         html  
    algo.farrington.assign.weights          html  
    algo.farrington.fitGLM                  html  
    algo.farrington.threshold               html  
    algo.glrnb                              html  
    algo.hhh                                html  
    algo.hhh.grid                           html  
    algo.hmm                                html  
    algo.outbreakP                          html  
    algo.quality                            html  
    algo.rki                                html  
    algo.rogerson                           html  
    algo.summary                            html  
    algo.twins                              html  
    all.equal                               html  
    animate                                 html  
    anscombe.residuals                      html  
    arlCusum                                html  
    backprojNP                              html  
    bestCombination                         html  
    boda                                    html  
    bodaDelay                               html  
    calibration                             html  
    campyDE                                 html  
    categoricalCUSUM                        html  
    checkResidualProcess                    html  
    clapply                                 html  
    coeflist                                html  
    create.disProg                          html  
    create.grid                             html  
    deleval                                 html  
    disProg2sts                             html  
    discpoly                                html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/discpoly.Rd:12: file link 'gpc.poly-class' in package 'rgeos' does not exist and so has been treated as a topic
    earsC                                   html  
    epidata                                 html  
    epidataCS                               html  
    finding level-2 HTML links ... done

    epidataCS_aggregate                     html  
    epidataCS_animate                       html  
    epidataCS_permute                       html  
    epidataCS_plot                          html  
    epidataCS_update                        html  
    epidata_animate                         html  
    epidata_intersperse                     html  
    epidata_plot                            html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/epidata_plot.Rd:56: file link 'brewer.pal' in package 'RColorBrewer' does not exist and so has been treated as a topic
    epidata_summary                         html  
    estimateGLRNbHook                       html  
    fanplot                                 html  
    farringtonFlexible                      html  
    find.kh                                 html  
    findH                                   html  
    findK                                   html  
    fluBYBW                                 html  
    formatDate                              html  
    formatPval                              html  
    glm_epidataCS                           html  
    ha                                      html  
    hagelloch                               html  
    hcl.colors                              html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/hcl.colors.Rd:8: file link 'heat_hcl' in package 'colorspace' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/hcl.colors.Rd:25: file link 'heat_hcl' in package 'colorspace' does not exist and so has been treated as a topic
    hepatitisA                              html  
    hhh4                                    html  
    hhh4_W                                  html  
    hhh4_W_utils                            html  
    hhh4_formula                            html  
    hhh4_internals                          html  
    hhh4_methods                            html  
    hhh4_plot                               html  
Rd warning: /tmp/RtmpZXeVmT/Rbuild1fcc29b2ef6f/surveillance/man/hhh4_plot.Rd:264: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
    hhh4_predict                            html  
    hhh4_simulate                           html  
    hhh4_simulate_plot                      html  
    hhh4_simulate_scores                    html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/hhh4_simulate_scores.Rd:53: file link 'logs_sample' in package 'scoringRules' does not exist and so has been treated as a topic
    hhh4_update                             html  
    hhh4_validation                         html  
Rd warning: /tmp/RtmpZXeVmT/Rbuild1fcc29b2ef6f/surveillance/man/hhh4_validation.Rd:103: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
    husO104Hosp                             html  
    imdepi                                  html  
    imdepifit                               html  
    influMen                                html  
    inside.gpc.poly                         html  
    intensityplot                           html  
    intersectPolyCircle                     html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/intersectPolyCircle.Rd:30: file link 'gIntersection' in package 'rgeos' does not exist and so has been treated as a topic
    isScalar                                html  
    isoWeekYear                             html  
    knox                                    html  
    ks.plot.unif                            html  
    layout.labels                           html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/layout.labels.Rd:37: file link 'panel.text' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/layout.labels.Rd:63: file link 'panel.text' in package 'lattice' does not exist and so has been treated as a topic
    linelist2sts                            html  
    loglikelihood                           html  
    m1                                      html  
    magic.dim                               html  
    make.design                             html  
    makeControl                             html  
    marks                                   html  
    meanResponse                            html  
    measles.weser                           html  
    measlesDE                               html  
    meningo.age                             html  
    momo                                    html  
    multiplicity                            html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/multiplicity.Rd:7: file link 'multiplicity' in package 'spatstat' does not exist and so has been treated as a topic
    multiplicity.Spatial                    html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/multiplicity.Spatial.Rd:36: file link 'multiplicity' in package 'spatstat' does not exist and so has been treated as a topic
    nbOrder                                 html  
    nowcast                                 html  
    pairedbinCUSUM                          html  
    permutationTest                         html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/permutationTest.Rd:68: file link 'symmetry_test' in package 'coin' does not exist and so has been treated as a topic
    pit                                     html  
    plapply                                 html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:7: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:7: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:25: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:26: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:34: file link 'clusterSetRNGStream' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:68: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/plapply.Rd:68: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    plot.atwins                             html  
    plot.disProg                            html  
    plot.survRes                            html  
    poly2adjmat                             html  
    polyAtBorder                            html  
    predict.ah                              html  
    primeFactors                            html  
    print.algoQV                            html  
    ranef                                   html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/ranef.Rd:9: file link 'ranef' in package 'nlme' does not exist and so has been treated as a topic
    refvalIdxByDate                         html  
    residuals.ah                            html  
    residualsCT                             html  
    rotaBB                                  html  
    runifdisc                               html  
    salmAllOnset                            html  
    salmHospitalized                        html  
    salmNewport                             html  
    salmonella.agona                        html  
    scale.gpc.poly                          html  
    scores                                  html  
    shadar                                  html  
    sim.pointSource                         html  
    sim.seasonalNoise                       html  
    simHHH                                  html  
    stK                                     html  
    stcd                                    html  
    sts-class                               html  
    stsAggregate                            html  
    stsBP-class                             html  
    stsNC-class                             html  
    stsNClist_animate                       html  
    stsNewport                              html  
    stsSlots                                html  
    stsXtrct                                html  
    sts_animate                             html  
    sts_creation                            html  
    sts_ggplot                              html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/sts_ggplot.Rd:30: file link 'geom_line' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/sts_ggplot.Rd:32: file link 'geom_col' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/sts_ggplot.Rd:36: file link 'geom_col' in package 'ggplot2' does not exist and so has been treated as a topic
    sts_observation                         html  
    sts_tidy                                html  
    stsplot                                 html  
    stsplot_space                           html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/stsplot_space.Rd:82: file link 'trans' in package 'scales' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/stsplot_space.Rd:94: file link 'heat_hcl' in package 'colorspace' does not exist and so has been treated as a topic
    stsplot_spacetime                       html  
    stsplot_time                            html  
    surveillance-defunct                    html  
    surveillance-deprecated                 html  
    surveillance-package                    html  
    surveillance.options                    html  
    toLatex.sts                             html  
    twinSIR                                 html  
    twinSIR_cox                             html  
    twinSIR_exData                          html  
    twinSIR_intensityplot                   html  
    twinSIR_methods                         html  
    twinSIR_profile                         html  
    twinSIR_simulation                      html  
    twinstim                                html  
Rd warning: /tmp/RtmpZXeVmT/Rbuild1fcc29b2ef6f/surveillance/man/twinstim.Rd:261: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
    twinstim_epitest                        html  
    twinstim_iaf                            html  
    twinstim_iafplot                        html  
    twinstim_intensity                      html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/twinstim_intensity.Rd:112: file link 'Sobj_SpatialGrid' in package 'maptools' does not exist and so has been treated as a topic
    twinstim_methods                        html  
    twinstim_plot                           html  
    twinstim_profile                        html  
    twinstim_siaf                           html  
    twinstim_siaf_simulatePC                html  
    twinstim_simEndemicEvents               html  
    twinstim_simulation                     html  
    twinstim_step                           html  
    twinstim_tiaf                           html  
    twinstim_update                         html  
    unionSpatialPolygons                    html  
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/unionSpatialPolygons.Rd:27: file link 'gUnaryUnion' in package 'rgeos' does not exist and so has been treated as a topic
Rd warning: R:/tmp/RtmpQRuPyX/R.INSTALLdbc8814bdd/surveillance/man/unionSpatialPolygons.Rd:49: file link 'gUnaryUnion' in package 'rgeos' does not exist and so has been treated as a topic
    untie                                   html  
    wrap.algo                               html  
    xtable.algoQV                           html  
    zetaweights                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'surveillance' as surveillance_1.17.0.9000.zip
* DONE (surveillance)
In R CMD INSTALL
Run time: 94.22 seconds.
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge