############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.42.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'cn.farms' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_cnfarms.c -o R_init_cnfarms.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c laplace.cpp -o laplace.o laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable] int method=0; ^~~~~~ laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)': laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized] double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right; ~~~~~~~~~~~~~~^~~~~~~~ laplace.cpp:393:86: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized] moment2 = (-0.5*a+0.25*(b-1/sigmaZ)*(b-1/sigmaZ)+(b*leftWeight)/(sigmaZ)+(leftWeight*I1left*sqrtMa)/(sqrt(2.0)*sigmaZ))/(a*a); ~~~~~~~~~~^~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse_farms.c -o sparse_farms.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -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/cn.farms.buildbin-libdir/00LOCK-cn.farms/00new/cn.farms/libs/i386 ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cn.farms' finding HTML links ... done callSummarize html cn.farms html cnLibrary html combineData html createAnnotation html createMatrix html distributionDistance html dnaCopySf html doCnFarmsSingle html flcSnp6Std html flcStd html fragLengCorr html getFragmentSet html getSingleProbeSetSize html mlSummarization html normAdd html normalizeAverage html normalizeCels html normalizeNone html normalizeNpData html normalizeQuantiles html normalizeSequenceEffect html normalizeSor html plotDendrogram html plotDensity html plotEvalIc html plotRegions html plotSmoothScatter html plotViolines html slSummarization html sparseFarmsC html summarizeFarmsExact html summarizeFarmsExact2 html summarizeFarmsExact3 html summarizeFarmsGaussian html summarizeFarmsMethods html summarizeFarmsStatistics html summarizeFarmsVariational html summarizeWindowBps html summarizeWindowMethods html summarizeWindowStd 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 'cn.farms' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_cnfarms.c -o R_init_cnfarms.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c laplace.cpp -o laplace.o laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable] int method=0; ^~~~~~ laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)': laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized] double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right; ~~~~~~~~~~~~~~^~~~~~~~ laplace.cpp:364:35: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized] double I2left=(-leftMy/leftSigma)*I1left+I0left; ~~~~~~~~~~~~~~~~~~~^~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse_farms.c -o sparse_farms.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -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/cn.farms.buildbin-libdir/cn.farms/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'cn.farms' as cn.farms_1.42.0.zip * DONE (cn.farms)