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###
### Running command:
###
###   rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.16.0.tar.gz
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install for i386

* installing *source* package 'motifcounter' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rbackground.c -o Rbackground.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcombinatorial.c -o Rcombinatorial.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rminmaxscore.c -o Rminmaxscore.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roption.c -o Roption.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roverlap.c -o Roverlap.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rscore1d.c -o Rscore1d.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsequence.c -o Rsequence.o
Rsequence.c: In function 'RscoreHistogram':
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
     int mins, maxs, noscores;
                     ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsimulate.c -o Rsimulate.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c background.c -o background.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c combinatorial.c -o combinatorial.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compoundpoisson.c -o compoundpoisson.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain.c -o markovchain.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain_single.c -o markovchain_single.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c matrix.c -o matrix.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mdist_register.c -o mdist_register.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c minmaxscore.c -o minmaxscore.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c overlap.c -o overlap.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score1d.c -o score1d.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score2d.c -o score2d.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c: In function 'getPositionWeights':
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
     int j, i, index, cindex, ds;
                      ^~~~~~
scorefunctions.c: In function 'hitSequence':
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
   int s, index, cindex;
                 ^~~~~~
scorefunctions.c: In function 'scoreSequence':
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
     int s, index, cindex;
                   ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sequence.c -o sequence.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o motifcounter.dll tmp.def Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -fopenmp -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/motifcounter.buildbin-libdir/00LOCK-motifcounter/00new/motifcounter/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'motifcounter'
    finding HTML links ... done
    Background-class                        html  
    Overlap-class                           html  
    clumpSizeDist                           html  
    combinatorialDist                       html  
    compoundPoissonDist                     html  
    computeClumpStartProb                   html  
    generateDNAString                       html  
    generateDNAStringSet                    html  
    getAlpha                                html  
    getBeta                                 html  
    getBeta3p                               html  
    getBeta5p                               html  
    getCounts                               html  
    getGamma                                html  
    getOrder                                html  
    getSinglestranded                       html  
    getStation                              html  
    getTrans                                html  
    hitStrand                               html  
    lenSequences                            html  
    markovModel                             html  
    motifAndBackgroundValid                 html  
    motifEnrichment                         html  
    motifHitProfile                         html  
    motifHits                               html  
    motifValid                              html  
    motifcounter-package                    html  
    motifcounterOptions                     html  
    normalizeMotif                          html  
    numMotifHits                            html  
    probOverlapHit                          html  
    readBackground                          html  
    revcompMotif                            html  
    scoreDist                               html  
    scoreDistBf                             html  
    scoreDistEmpirical                      html  
    scoreHistogram                          html  
    scoreHistogramSingleSeq                 html  
    scoreProfile                            html  
    scoreSequence                           html  
    scoreStrand                             html  
    scoreThreshold                          html  
    sigLevel                                html  
    simulateClumpSizeDist                   html  
    simulateNumHitsDist                     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 'motifcounter' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rbackground.c -o Rbackground.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcombinatorial.c -o Rcombinatorial.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rminmaxscore.c -o Rminmaxscore.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roption.c -o Roption.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roverlap.c -o Roverlap.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rscore1d.c -o Rscore1d.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsequence.c -o Rsequence.o
Rsequence.c: In function 'RscoreHistogram':
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
     int mins, maxs, noscores;
                     ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsimulate.c -o Rsimulate.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c background.c -o background.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c combinatorial.c -o combinatorial.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compoundpoisson.c -o compoundpoisson.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain.c -o markovchain.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain_single.c -o markovchain_single.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c matrix.c -o matrix.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mdist_register.c -o mdist_register.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c minmaxscore.c -o minmaxscore.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c overlap.c -o overlap.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score1d.c -o score1d.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score2d.c -o score2d.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c: In function 'getPositionWeights':
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
     int j, i, index, cindex, ds;
                      ^~~~~~
scorefunctions.c: In function 'hitSequence':
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
   int s, index, cindex;
                 ^~~~~~
scorefunctions.c: In function 'scoreSequence':
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
     int s, index, cindex;
                   ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sequence.c -o sequence.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o motifcounter.dll tmp.def Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -fopenmp -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/motifcounter.buildbin-libdir/motifcounter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifcounter' as motifcounter_1.16.0.zip
* DONE (motifcounter)