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### Running command:
###
###   rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=flowClust.buildbin-libdir flowClust_3.33.0.tar.gz
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* installing *source* package 'flowClust' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
rm -f BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust.dll
"D:/biocbuild/bbs-3.15-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.4
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c BoxCox.c -o BoxCox.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
  rowPrecision, rowZ, rowLambda0;
                ^~~~
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
  double *nu0 = p->nu0, kappa0 = p->kappa0;
                        ^~~~~~
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
  int *itersolve = p->itersolve;
       ^~~~~~~~~
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
  int iter = p->iter;
      ^~~~
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
  int model = *p->model;
      ^~~~~
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
  gsl_vector *SumZlogY = p->SumZlogY;
              ^~~~~~~~
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
  gsl_matrix *Precision = p->Precision; // will be updated
              ^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Nu.c -o Nu.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
  matrixZUY2;
  ^~~~~~~~~~
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
                                                ^~~~~~~~~~
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
  rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
                                       ^~~~~~~
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
  int i=0;
      ^
At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
 static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
                           ^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:702:13: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
    status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:15: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       nu_hi = gsl_root_fsolver_x_upper(s2);
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x_hi = gsl_root_fsolver_x_upper(s);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:14: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x_hi = gsl_root_fsolver_x_upper(s);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ranMVNT.c -o ranMVNT.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L../windows/gsl-2.4/lib/x64 -lgsl -lgslcblas -lm -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/flowClust.buildbin-libdir/00LOCK-flowClust/00new/flowClust/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'Map' in package 'flowClust'
** help
*** installing help indices
  converting help for package 'flowClust'
    finding HTML links ... done
    BIC                                     html  
    Map                                     html  
    SimulateMixture                         html  
    Subset                                  html  
    box                                     html  
    density                                 html  
    dmvt                                    html  
    dmvtmix                                 html  
    flowClust-package                       html  
    flowClust                               html  
    flowClust.den                           html  
    flowClust2Prior                         html  
    hist                                    html  
    miscellaneous                           html  
    mkPrior                                 html  
    peakMatch                               html  
    plot.flowClust                          html  
    plot.flowCore                           html  
    plot.flowDens                           html  
    plotPrior                               html  
    rbox                                    html  
    rituximab                               html  
    ruleOutliers                            html  
    show.flowClust                          html  
    split                                   html  
    summary                                 html  
    tmixFilter                              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 'flowClust' as flowClust_3.33.0.zip
* DONE (flowClust)