############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL snapCGH ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'snapCGH' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c optimizer.c -o optimizer.o optimizer.c: In function 'fr_two': optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c: In function 'fr_three': optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1]; ^~~~~~~~ optimizer.c: In function 'fr_four': optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1]; ^~~~~~~~ optimizer.c: In function 'fr_five': optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1]; ^~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-snapCGH/00new/snapCGH/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'snapCGH' finding HTML links ... done IDProbes html LargeDataObject html SegList html Viterbi.five html Viterbi.four html Viterbi.three html Viterbi.two html cbind html chrominfo.Mb html compareSegmentations html convert.output html dim html dimnames html filter html find.param.five html find.param.four html find.param.one html find.param.three html find.param.two html findBreakPoints html fit.model html genomePlot html heatmapGenome html imputeMissingValues html log2ratios html mergeStates html plotSegmentedGenome html processCGH html read.clonesinfo html readPositionalInfo html removeByWeights html runBioHMM html runDNAcopy html runGLAD html runHMM html runTilingArray html sim.structure html zoomChromosome html zoomGenome 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 * DONE (snapCGH) Making 'packages.html' ... done