* installing *source* package ‘scellpam’ ... ** package ‘scellpam’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/scellpam/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c biodatatojmat.cpp -o biodatatojmat.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c buildresults.cpp -o buildresults.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c csvtojmat.cpp -o csvtojmat.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c debugpar.cpp -o debugpar.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c diftimehelper.cpp -o diftimehelper.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c dissimmat.cpp -o dissimmat.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c dissimmat_full.cpp -o dissimmat_full.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c dissimmat_sparse.cpp -o dissimmat_sparse.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fastpam.cpp -o fastpam.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c filternames.cpp -o filternames.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c filtersil.cpp -o filtersil.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fullmatrix.cpp -o fullmatrix.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c jmatrix.cpp -o jmatrix.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c jmatrixaux.cpp -o jmatrixaux.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c mainfastpam.cpp -o mainfastpam.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c matgetcols.cpp -o matgetcols.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c matgetdiag.cpp -o matgetdiag.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c matgetrows.cpp -o matgetrows.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c matinfo.cpp -o matinfo.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c matmetadata.cpp -o matmetadata.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c matwrite.cpp -o matwrite.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c memhelper.cpp -o memhelper.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c silhouette.cpp -o silhouette.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c sparsematrix.cpp -o sparsematrix.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c symmetricmatrix.cpp -o symmetricmatrix.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c threadhelper.cpp -o threadhelper.o /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o scellpam.so RcppExports.o biodatatojmat.o buildresults.o csvtojmat.o debugpar.o diftimehelper.o dissimmat.o dissimmat_full.o dissimmat_sparse.o fastpam.o filternames.o filtersil.o fullmatrix.o jmatrix.o jmatrixaux.o mainfastpam.o matgetcols.o matgetdiag.o matgetrows.o matinfo.o matmetadata.o matwrite.o memhelper.o silhouette.o sparsematrix.o symmetricmatrix.o threadhelper.o -lpthread -O2 make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/scellpam/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/scellpam/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/scellpam/src' installing to /data/gannet/ripley/R/packages/tests-clang/scellpam.Rcheck/00LOCK-scellpam/00new/scellpam/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 (scellpam)