* installing *source* package ‘qtl’ ...
** package ‘qtl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 17.0.5’
using C++ compiler: ‘clang version 17.0.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/qtl/src'
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c R_init.c -o R_init.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c countXO.c -o countXO.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c discan.c -o discan.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c discan_covar.c -o discan_covar.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c effectscan.c -o effectscan.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c fill_geno_nodblXO.c -o fill_geno_nodblXO.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c findDupMarkers_notexact.c -o findDupMarkers_notexact.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c fitqtl_hk.c -o fitqtl_hk.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c fitqtl_hk_binary.c -o fitqtl_hk_binary.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c fitqtl_imp.c -o fitqtl_imp.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c fitqtl_imp_binary.c -o fitqtl_imp_binary.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c forwsel.c -o forwsel.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_4way.c -o hmm_4way.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_bc.c -o hmm_bc.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_bci.c -o hmm_bci.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_bcsft.c -o hmm_bcsft.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_bgmagic16.c -o hmm_bgmagic16.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_f2.c -o hmm_f2.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_f2i.c -o hmm_f2i.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_main.c -o hmm_main.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_ri4self.c -o hmm_ri4self.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_ri4sib.c -o hmm_ri4sib.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_ri8self.c -o hmm_ri8self.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_ri8selfIRIP1.c -o hmm_ri8selfIRIP1.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_ri8sib.c -o hmm_ri8sib.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hmm_util.c -o hmm_util.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c inferFounderHap.c -o inferFounderHap.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c info.c -o info.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c lapackutil.c -o lapackutil.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c markerlrt.c -o markerlrt.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmaugment.cpp -o mqmaugment.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmdatatypes.cpp -o mqmdatatypes.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmeliminate.cpp -o mqmeliminate.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmmapqtl.cpp -o mqmmapqtl.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmmixture.cpp -o mqmmixture.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmprob.cpp -o mqmprob.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmregression.cpp -o mqmregression.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -c mqmscan.cpp -o mqmscan.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c pickMarkerSubset.c -o pickMarkerSubset.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c ril48_reorg.c -o ril48_reorg.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c ripple.c -o ripple.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_ehk.c -o scanone_ehk.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_em.c -o scanone_em.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_em_covar.c -o scanone_em_covar.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_hk.c -o scanone_hk.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_hk_binary.c -o scanone_hk_binary.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_imp.c -o scanone_imp.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_mr.c -o scanone_mr.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scanone_np.c -o scanone_np.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwo_binary_em.c -o scantwo_binary_em.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwo_binary_hk.c -o scantwo_binary_hk.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwo_em.c -o scantwo_em.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwo_hk.c -o scantwo_hk.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwo_imp.c -o scantwo_imp.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwo_mr.c -o scantwo_mr.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c scantwopermhk.c -o scantwopermhk.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c simulate.c -o simulate.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c simulate_ril.c -o simulate_ril.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c stahl_mf.c -o stahl_mf.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c summary_scantwo.c -o summary_scantwo.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c test_bcsft.c -o test_bcsft.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c util.c -o util.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c vbscan.c -o vbscan.o
/usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang17/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c zeroin.c -o zeroin.o
/usr/local/clang17/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang17/lib -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o qtl.so 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 -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/qtl/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/qtl/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/qtl/src'
installing to /data/gannet/ripley/R/packages/tests-clang/qtl.Rcheck/00LOCK-qtl/00new/qtl/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qtl)