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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL flowClust
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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/R/library/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  
    Subset                                  html  
    box                                     html  
    density                                 html  
    dmvt                                    html  
    dmvtmix                                 html  
    flowClust-package                       html  
    flowClust                               html  
    finding level-2 HTML links ... done

Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/flowClust/man/flowClust.Rd:290: missing link 'SimulateMixture'
    flowClust.den                           html  
    hist                                    html  
    miscellaneous                           html  
    plot.flowClust                          html  
    plot.flowCore                           html  
    plot.flowDens                           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
* DONE (flowClust)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'topconfects' is missing or broken
 done