##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=Repitools.buildbin-libdir Repitools_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'Repitools' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c const.c -o const.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:
./mconf.h:100: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:42,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:29: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 
In file included from hyp2f1.c:81:
./mconf.h:101: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:42,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:30: note: this is the location of the previous definition
 #define SING  _SING
 
In file included from hyp2f1.c:81:
./mconf.h:102: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:42,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:31: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 
In file included from hyp2f1.c:81:
./mconf.h:103: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:42,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:32: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 
In file included from hyp2f1.c:81:
./mconf.h:104: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:42,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:33: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 
In file included from hyp2f1.c:81:
./mconf.h:105: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:42,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:34: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:
./mconf.h:100: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:29: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 
In file included from mtherr.c:58:
./mconf.h:101: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:30: note: this is the location of the previous definition
 #define SING  _SING
 
In file included from mtherr.c:58:
./mconf.h:102: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:31: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 
In file included from mtherr.c:58:
./mconf.h:103: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:32: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 
In file included from mtherr.c:58:
./mconf.h:104: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:33: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 
In file included from mtherr.c:58:
./mconf.h:105: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:34: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -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/Repitools.buildbin-libdir/00LOCK-Repitools/00new/Repitools/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Repitools'
    finding HTML links ... done
    AdjustedCopyEstimate-class              html  
    finding level-2 HTML links ... done

    AffymetrixCdfFile-class                 html  
    AffymetrixCelSet-class                  html  
    BAM2GRanges                             html  
    BayMethList-class                       html  
    ChromaBlocks                            html  
    ChromaResults-class                     html  
    ClusteredScoresList-class               html  
    CopyEstimate-class                      html  
    FastQC-class                            html  
    GCAdjustParams-class                    html  
    GCadjustCopy                            html  
    GCbiasPlots                             html  
    MappabilitySource-class                 html  
    QdnaData                                html  
    ScoresList-class                        html  
    abcdDNA                                 html  
    absoluteCN                              html  
    annoDF2GR                               html  
    annoGR2DF                               html  
    annotationBlocksCounts                  html  
    annotationBlocksLookup                  html  
    annotationCounts                        html  
    annotationLookup                        html  
    binPlots                                html  
    blocksStats                             html  
    checkProbes                             html  
    chr21genes                              html  
    chromosomeCNplots                       html  
    clusterPlots                            html  
    cpgBoxPlots                             html  
    cpgDensityCalc                          html  
    cpgDensityPlot                          html  
    determineOffset                         html  
    empBayes                                html  
    enrichmentCalc                          html  
    enrichmentPlot                          html  
    expr                                    html  
    featureBlocks                           html  
    featureScores                           html  
    findClusters                            html  
    gcContentCalc                           html  
    genQC                                   html  
    genomeBlocks                            html  
    getProbePositionsDf                     html  
    getSampleOffsets                        html  
    hcRegions                               html  
    hyper                                   html  
    loadPairFile                            html  
    loadSampleDirectory                     html  
    makeWindowLookupTable                   html  
    mappabilityCalc                         html  
    maskOut                                 html  
    mergeReplicates                         html  
    methylEst                               html  
    multiHeatmap                            html  
    plotClusters                            html  
    plotQdnaByCN                            html  
    processNDF                              html  
    profilePlots                            html  
    regionStats                             html  
    relativeCN                              html  
    samplesList                             html  
    sequenceCalc                            html  
    setCNVOffsets                           html  
    summarizeScores                         html  
    writeWig                                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 'Repitools' as Repitools_1.41.1.zip
* DONE (Repitools)