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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL flowClust
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'flowClust' ...
** using staged installation

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


** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
rm -f BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust.dll
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/src/include     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BoxCox.c -o BoxCox.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/src/include     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:23: warning: unused variable 'rowZ' [-Wunused-variable]
   57 |         rowPrecision, rowZ, rowLambda0;
      |                       ^~~~
BoxCoxPriors.c:33:31: warning: unused variable 'kappa0' [-Wunused-variable]
   33 |         double *nu0 = p->nu0, kappa0 = p->kappa0;
      |                               ^~~~~~
BoxCoxPriors.c:32:14: warning: unused variable 'itersolve' [-Wunused-variable]
   32 |         int *itersolve = p->itersolve;
      |              ^~~~~~~~~
BoxCoxPriors.c:31:13: warning: unused variable 'iter' [-Wunused-variable]
   31 |         int iter = p->iter;
      |             ^~~~
BoxCoxPriors.c:28:13: warning: unused variable 'model' [-Wunused-variable]
   28 |         int model = *p->model;
      |             ^~~~~
BoxCoxPriors.c:23:21: warning: unused variable 'SumZlogY' [-Wunused-variable]
   23 |         gsl_vector *SumZlogY = p->SumZlogY;
      |                     ^~~~~~~~
BoxCoxPriors.c:15:21: warning: unused variable 'Precision' [-Wunused-variable]
   15 |         gsl_matrix *Precision = p->Precision; // will be updated
      |                     ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/src/include     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Nu.c -o Nu.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/src/include     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:9: warning: unused variable 'matrixZUY2' [-Wunused-variable]
   48 |         matrixZUY2;
      |         ^~~~~~~~~~
flowClust.c:46:55: warning: unused variable 'subRowZUY2' [-Wunused-variable]
   46 |         rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
      |                                                       ^~~~~~~~~~
flowClust.c:46:46: warning: unused variable 'rowZUY2' [-Wunused-variable]
   46 |         rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
      |                                              ^~~~~~~
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:13: warning: unused variable 'i' [-Wunused-variable]
 1111 |         int i=0;
      |             ^
flowClust.c: At top level:
flowClust.c:10:27: warning: 'CEntries' defined but not used [-Wunused-const-variable=]
   10 | static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
      |                           ^~~~~~~~
flowClust.c: In function 'flowClust':
flowClust.c:713:49: warning: 's3' may be used uninitialized [-Wmaybe-uninitialized]
  713 |                                         nu_hi = gsl_min_fminimizer_x_upper(s3);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:61:29: note: 's3' was declared here
   61 |         gsl_min_fminimizer *s3; // pointer to a newly allocated instance of a minimizer
      |                             ^~
flowClust.c:647:57: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized]
  647 |                                                 nu_hi = gsl_root_fsolver_x_upper(s2);
      |                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:59:31: note: 's2' was declared here
   59 |         gsl_root_fsolver *s, *s2; // pointer to a newly allocated instance of a solver
      |                               ^~
flowClust.c:348:56: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
  348 |                                                 x_hi = gsl_root_fsolver_x_upper(s);
      |                                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:59:27: note: 's' was declared here
   59 |         gsl_root_fsolver *s, *s2; // pointer to a newly allocated instance of a solver
      |                           ^
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/src/include     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:207:56: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
  207 |                                                 x_hi = gsl_root_fsolver_x_upper(s);
      |                                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClustGaussian.c:39:27: note: 's' was declared here
   39 |         gsl_root_fsolver *s; // pointer to a newly allocated instance of a solver
      |                           ^
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/src/include     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ranMVNT.c -o ranMVNT.o
gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -lgsl -lgslcblas -lm -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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
** 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)