############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cn.farms_1.42.0.tar.gz && 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 && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cn.farms_1.42.0.zip && rm cn.farms_1.42.0.tar.gz cn.farms_1.42.0.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 10 2055k 10 218k 0 0 642k 0 0:00:03 --:--:-- 0:00:03 641k 82 2055k 82 1696k 0 0 1295k 0 0:00:01 0:00:01 --:--:-- 1296k 100 2055k 100 2055k 0 0 1375k 0 0:00:01 0:00:01 --:--:-- 1376k 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) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'cn.farms' successfully unpacked and MD5 sums checked