* installing *source* package 'qtl' ... ** package 'qtl' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'g++.exe (GCC) 13.2.0' make[1]: Entering directory '/d/temp/Rtmp6NMDZR/R.INSTALL13ec3dfc22eb/qtl/src' gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init.c -o R_init.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c countXO.c -o countXO.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c discan.c -o discan.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c discan_covar.c -o discan_covar.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c effectscan.c -o effectscan.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_geno_nodblXO.c -o fill_geno_nodblXO.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findDupMarkers_notexact.c -o findDupMarkers_notexact.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitqtl_hk.c -o fitqtl_hk.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitqtl_hk_binary.c -o fitqtl_hk_binary.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitqtl_imp.c -o fitqtl_imp.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitqtl_imp_binary.c -o fitqtl_imp_binary.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c forwsel.c -o forwsel.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_4way.c -o hmm_4way.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_bc.c -o hmm_bc.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_bci.c -o hmm_bci.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_bcsft.c -o hmm_bcsft.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_bgmagic16.c -o hmm_bgmagic16.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_f2.c -o hmm_f2.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_f2i.c -o hmm_f2i.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_main.c -o hmm_main.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_ri4self.c -o hmm_ri4self.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_ri4sib.c -o hmm_ri4sib.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_ri8self.c -o hmm_ri8self.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_ri8selfIRIP1.c -o hmm_ri8selfIRIP1.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_ri8sib.c -o hmm_ri8sib.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_util.c -o hmm_util.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inferFounderHap.c -o inferFounderHap.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c info.c -o info.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lapackutil.c -o lapackutil.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c markerlrt.c -o markerlrt.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmaugment.cpp -o mqmaugment.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmdatatypes.cpp -o mqmdatatypes.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmeliminate.cpp -o mqmeliminate.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmmapqtl.cpp -o mqmmapqtl.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmmixture.cpp -o mqmmixture.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmprob.cpp -o mqmprob.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmregression.cpp -o mqmregression.o g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqmscan.cpp -o mqmscan.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pickMarkerSubset.c -o pickMarkerSubset.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ril48_reorg.c -o ril48_reorg.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ripple.c -o ripple.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_ehk.c -o scanone_ehk.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_em.c -o scanone_em.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_em_covar.c -o scanone_em_covar.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_hk.c -o scanone_hk.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_hk_binary.c -o scanone_hk_binary.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_imp.c -o scanone_imp.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_mr.c -o scanone_mr.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scanone_np.c -o scanone_np.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwo_binary_em.c -o scantwo_binary_em.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwo_binary_hk.c -o scantwo_binary_hk.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwo_em.c -o scantwo_em.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwo_hk.c -o scantwo_hk.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwo_imp.c -o scantwo_imp.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwo_mr.c -o scantwo_mr.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scantwopermhk.c -o scantwopermhk.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulate.c -o simulate.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulate_ril.c -o simulate_ril.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stahl_mf.c -o stahl_mf.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c summary_scantwo.c -o summary_scantwo.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test_bcsft.c -o test_bcsft.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vbscan.c -o vbscan.o gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zeroin.c -o zeroin.o g++ -std=gnu++17 -shared -s -static-libgcc -o qtl.dll tmp.def R_init.o countXO.o discan.o discan_covar.o effectscan.o fill_geno_nodblXO.o findDupMarkers_notexact.o fitqtl_hk.o fitqtl_hk_binary.o fitqtl_imp.o fitqtl_imp_binary.o forwsel.o hmm_4way.o hmm_bc.o hmm_bci.o hmm_bcsft.o hmm_bgmagic16.o hmm_f2.o hmm_f2i.o hmm_main.o hmm_ri4self.o hmm_ri4sib.o hmm_ri8self.o hmm_ri8selfIRIP1.o hmm_ri8sib.o hmm_util.o inferFounderHap.o info.o lapackutil.o markerlrt.o mqmaugment.o mqmdatatypes.o mqmeliminate.o mqmmapqtl.o mqmmixture.o mqmprob.o mqmregression.o mqmscan.o pickMarkerSubset.o ril48_reorg.o ripple.o scanone_ehk.o scanone_em.o scanone_em_covar.o scanone_hk.o scanone_hk_binary.o scanone_imp.o scanone_mr.o scanone_np.o scantwo_binary_em.o scantwo_binary_hk.o scantwo_em.o scantwo_hk.o scantwo_imp.o scantwo_mr.o scantwopermhk.o simulate.o simulate_ril.o stahl_mf.o summary_scantwo.o test_bcsft.o util.o vbscan.o zeroin.o -LD:/RCompile/recent/R-4.4.0/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.0/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.0/bin/x64 -lR make[1]: Leaving directory '/d/temp/Rtmp6NMDZR/R.INSTALL13ec3dfc22eb/qtl/src' make[1]: Entering directory '/d/temp/Rtmp6NMDZR/R.INSTALL13ec3dfc22eb/qtl/src' make[1]: Leaving directory '/d/temp/Rtmp6NMDZR/R.INSTALL13ec3dfc22eb/qtl/src' installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-qtl/00new/qtl/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * MD5 sums packaged installation of 'qtl' as qtl_1.66.zip * DONE (qtl)