############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SNPRelate_1.26.0.tar.gz && rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPRelate.buildbin-libdir SNPRelate_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SNPRelate_1.26.0.zip && rm SNPRelate_1.26.0.tar.gz SNPRelate_1.26.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1206k 100 1206k 0 0 2991k 0 --:--:-- --:--:-- --:--:-- 3000k install for i386 * installing *source* package 'SNPRelate' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SNPRelate.c -o R_SNPRelate.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPRelate.cpp -o SNPRelate.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadPool.cpp -o ThreadPool.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dGenGWAS.cpp -o dGenGWAS.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dVect.cpp -o dVect.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genBeta.cpp -o genBeta.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genEIGMIX.cpp -o genEIGMIX.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genFst.cpp -o genFst.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genHWE.cpp -o genHWE.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBD.cpp -o genIBD.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBS.cpp -o genIBS.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genKING.cpp -o genKING.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genLD.cpp -o genLD.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genPCA.cpp -o genPCA.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genSlideWin.cpp -o genSlideWin.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SNPRelate.buildbin-libdir/00LOCK-SNPRelate/00new/SNPRelate/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SNPRelate' finding HTML links ... done SNPGDSFileClass-class html SNPRelate-package html hapmap_geno html snpgdsAdmixPlot html snpgdsAdmixProp html snpgdsAlleleSwitch html snpgdsApartSelection html snpgdsBED2GDS html finding level-2 HTML links ... done snpgdsClose html snpgdsCombineGeno html snpgdsCreateGeno html snpgdsCreateGenoSet html snpgdsCutTree html snpgdsDiss html snpgdsDrawTree html snpgdsEIGMIX html snpgdsErrMsg html snpgdsExampleFileName html snpgdsFst html snpgdsGDS2BED html snpgdsGDS2Eigen html snpgdsGDS2PED html snpgdsGEN2GDS html snpgdsGRM html snpgdsGetGeno html snpgdsHCluster html snpgdsHWE html snpgdsIBDKING html snpgdsIBDMLE html snpgdsIBDMLELogLik html snpgdsIBDMoM html snpgdsIBDSelection html snpgdsIBS html snpgdsIBSNum html snpgdsIndInb html snpgdsIndInbCoef html snpgdsIndivBeta html snpgdsLDMat html snpgdsLDpair html snpgdsLDpruning html snpgdsMergeGRM html snpgdsOpen html snpgdsOption html snpgdsPCA html snpgdsPCACorr html snpgdsPCASNPLoading html snpgdsPCASampLoading html snpgdsPED2GDS html snpgdsPairIBD html snpgdsPairIBDMLELogLik html snpgdsPairScore html snpgdsSNPList html snpgdsSNPListClass html snpgdsSNPListIntersect html snpgdsSNPRateFreq html snpgdsSampMissRate html snpgdsSelectSNP html snpgdsSlidingWindow html snpgdsSummary html snpgdsTranspose html snpgdsVCF2GDS html snpgdsVCF2GDS_R 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 'SNPRelate' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SNPRelate.c -o R_SNPRelate.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPRelate.cpp -o SNPRelate.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadPool.cpp -o ThreadPool.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dGenGWAS.cpp -o dGenGWAS.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dVect.cpp -o dVect.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genBeta.cpp -o genBeta.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genEIGMIX.cpp -o genEIGMIX.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genFst.cpp -o genFst.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genHWE.cpp -o genHWE.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBD.cpp -o genIBD.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBS.cpp -o genIBS.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genKING.cpp -o genKING.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genLD.cpp -o genLD.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genPCA.cpp -o genPCA.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genSlideWin.cpp -o genSlideWin.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SNPRelate.buildbin-libdir/SNPRelate/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SNPRelate' as SNPRelate_1.26.0.zip * DONE (SNPRelate) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'SNPRelate' successfully unpacked and MD5 sums checked