* installing *source* package ‘hsphase’ ... ** this is package ‘hsphase’ version ‘2.0.4’ ** package ‘hsphase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 21.1.1’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hsphase/src' /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c FastDist.cpp -o FastDist.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c MAF.cpp -o MAF.o In file included from MAF.cpp:23: In file included from ./MAF.h:27: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages] 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Ohd.cpp -o Ohd.o In file included from Ohd.cpp:24: In file included from ./Ohd.h:27: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages] 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ 1 warning generated. 1 warning generated. /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c TypeConversion.cpp -o TypeConversion.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c block.cpp -o block.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c block4Phase.cpp -o block4Phase.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c co.cpp -o co.o In file included from co.cpp:24: In file included from ./co.h:26: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages] 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c diag.cpp -o diag.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c hsp.cpp -o hsp.o 1 warning generated. /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c main.cpp -o main.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c memory.cpp -o memory.o /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c oh.cpp -o oh.o In file included from oh.cpp:17: In file included from ./oh.h:20: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages] 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ /usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c swDetect.cpp -o swDetect.o 1 warning generated. /usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o hsphase.so FastDist.o MAF.o Ohd.o TypeConversion.o block.o block4Phase.o co.o diag.o hsp.o main.o memory.o oh.o swDetect.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm -fopenmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hsphase/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hsphase/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hsphase/src' installing to /data/gannet/ripley/R/packages/tests-clang/hsphase.Rcheck/00LOCK-hsphase/00new/hsphase/libs ** R ** data ** demo ** 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 (hsphase)