* installing *source* package ‘statgenIBD’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 17.0.6 (5)’ rm -f calcIBD.o RcppExports.o general/HMMalgo.o general/InhVector.o general/ibdexcept.o general/misc.o general/OrdGeno.o general/TransMatSym2D.o general/util_genetics.o pedigree/analysis_fam.o pedigree/crosses.o pedigree/Loc.o pedigree/mainR.o pedigree/markerscore.o pedigree/popt.o pedigree/read_map.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c calcIBD.cpp -o calcIBD.o calcIBD.cpp:109:19: warning: unused variable 'popt' [-Wunused-variable] 109 | const pop_base *popt = init_pop(_poptype); | ^~~~ 1 warning generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/HMMalgo.cpp -o general/HMMalgo.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/InhVector.cpp -o general/InhVector.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/ibdexcept.cpp -o general/ibdexcept.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/misc.cpp -o general/misc.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/OrdGeno.cpp -o general/OrdGeno.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/TransMatSym2D.cpp -o general/TransMatSym2D.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c general/util_genetics.cpp -o general/util_genetics.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/analysis_fam.cpp -o pedigree/analysis_fam.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/crosses.cpp -o pedigree/crosses.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/Loc.cpp -o pedigree/Loc.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/mainR.cpp -o pedigree/mainR.o pedigree/mainR.cpp:209:7: warning: variable 'Nfnd' set but not used [-Wunused-but-set-variable] 209 | int Nfnd = 0; | ^ 1 warning generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/markerscore.cpp -o pedigree/markerscore.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/popt.cpp -o pedigree/popt.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pedigree/read_map.cpp -o pedigree/read_map.o clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o statgenIBD.so calcIBD.o RcppExports.o general/HMMalgo.o general/InhVector.o general/ibdexcept.o general/misc.o general/OrdGeno.o general/TransMatSym2D.o general/util_genetics.o pedigree/analysis_fam.o pedigree/crosses.o pedigree/Loc.o pedigree/mainR.o pedigree/markerscore.o pedigree/popt.o pedigree/read_map.o -llapack -L/home/hornik/tmp/R/lib -lRblas -L/usr/lib/llvm-17/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/statgenIBD.Rcheck/00LOCK-statgenIBD/00new/statgenIBD/libs ** R ** 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 (statgenIBD)