############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL flowClust ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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) 13.3.0' rm -f BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o flowClust.dll gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BoxCox.c -o BoxCox.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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-3.20-bioc/R/include" -DNDEBUG -I/src/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Nu.c -o Nu.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:372:50: warning: 's' may be used uninitialized [-Wmaybe-uninitialized] 372 | status = gsl_root_fsolver_set(s, &F, *xLow, *xUp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flowClust.c:59:27: note: 's' was declared here 59 | gsl_root_fsolver *s, *s2; // pointer to a newly allocated instance of a solver | ^ flowClust.c:663:50: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized] 663 | status = gsl_root_fsolver_set(s2, &F2, *nuLow, *nuUp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:702:34: warning: 's3' may be used uninitialized [-Wmaybe-uninitialized] 702 | status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flowClust.c:61:29: note: 's3' was declared here 61 | gsl_min_fminimizer *s3; // pointer to a newly allocated instance of a minimizer | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c flowClustGaussian.c -o flowClustGaussian.o flowClustGaussian.c: In function 'flowClustGaussian': flowClustGaussian.c:230:50: warning: 's' may be used uninitialized [-Wmaybe-uninitialized] 230 | status = gsl_root_fsolver_set(s, &F, *xLow, *xUp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-3.20-bioc/R/include" -DNDEBUG -I/src/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-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)