############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowClust_3.32.0.tar.gz && rm -rf flowClust.buildbin-libdir && mkdir flowClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClust.buildbin-libdir flowClust_3.32.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowClust_3.32.0.zip && rm flowClust_3.32.0.tar.gz flowClust_3.32.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 2 1610k 2 33537 0 0 212k 0 0:00:07 --:--:-- 0:00:07 211k 57 1610k 57 921k 0 0 797k 0 0:00:02 0:00:01 0:00:01 796k 100 1610k 100 1610k 0 0 1006k 0 0:00:01 0:00:01 --:--:-- 1005k install for i386 * 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 "C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386/Rscript.exe" "../tools/winlibs.R" 2.4 "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BoxCox.c -o BoxCox.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Nu.c -o Nu.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ranMVNT.c -o ranMVNT.o C:/rtools40/mingw32/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/i386 -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/flowClust.buildbin-libdir/00LOCK-flowClust/00new/flowClust/libs/i386 ** 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 install for x64 * installing *source* package 'flowClust' ... ********************************************** 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 "C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.4 "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BoxCox.c -o BoxCox.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Nu.c -o Nu.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I../windows/gsl-2.4/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/flowClust.buildbin-libdir/flowClust/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'flowClust' as flowClust_3.32.0.zip * DONE (flowClust) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'flowClust' successfully unpacked and MD5 sums checked