* installing *source* package ‘scellpam’ ... ** package ‘scellpam’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/scellpam/src' /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c RcppExports.cpp -o RcppExports.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c biodatatojmat.cpp -o biodatatojmat.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c buildresults.cpp -o buildresults.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c csvtojmat.cpp -o csvtojmat.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c debugpar.cpp -o debugpar.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c diftimehelper.cpp -o diftimehelper.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c dissimmat.cpp -o dissimmat.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c dissimmat_full.cpp -o dissimmat_full.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c dissimmat_sparse.cpp -o dissimmat_sparse.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c fastpam.cpp -o fastpam.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c filternames.cpp -o filternames.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c filtersil.cpp -o filtersil.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c fullmatrix.cpp -o fullmatrix.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c jmatrix.cpp -o jmatrix.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c jmatrixaux.cpp -o jmatrixaux.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c mainfastpam.cpp -o mainfastpam.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c matgetcols.cpp -o matgetcols.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c matgetdiag.cpp -o matgetdiag.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c matgetrows.cpp -o matgetrows.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c matinfo.cpp -o matinfo.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c matmetadata.cpp -o matmetadata.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c matwrite.cpp -o matwrite.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c memhelper.cpp -o memhelper.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c silhouette.cpp -o silhouette.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c sparsematrix.cpp -o sparsematrix.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c symmetricmatrix.cpp -o symmetricmatrix.o /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -I"/data/gannet/ripley/R/Intel/include" -DNDEBUG -I'/data/gannet2/ripley/R/test-MKL/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -O3 -fp-model precise -Wall -c threadhelper.cpp -o threadhelper.o In file included from sparsematrix.cpp:19: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/Rcpp.h:27: In file included from /data/gannet2/ripley/R/test-MKL/Rcpp/include/RcppCommon.h:62: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/functional:64: In file included from /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:61: /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:263:8: warning: 'get_temporary_buffer' is deprecated [-Wdeprecated-declarations] 263 | std::get_temporary_buffer(_M_original_len)); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:4996:15: note: in instantiation of member function 'std::_Temporary_buffer<__gnu_cxx::__normal_iterator>, unsigned long>::_Temporary_buffer' requested here 4996 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_algo.h:5070:23: note: in instantiation of function template specialization 'std::__stable_sort<__gnu_cxx::__normal_iterator>, __gnu_cxx::__ops::_Iter_comp_iter<(lambda at sparsematrix.cpp:35:8)>>' requested here 5070 | _GLIBCXX_STD_A::__stable_sort(__first, __last, | ^ sparsematrix.cpp:34:3: note: in instantiation of function template specialization 'std::stable_sort<__gnu_cxx::__normal_iterator>, (lambda at sparsematrix.cpp:35:8)>' requested here 34 | stable_sort(idx.begin(), idx.end(), | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:99:5: note: 'get_temporary_buffer' has been explicitly marked deprecated here 99 | _GLIBCXX17_DEPRECATED | ^ /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/x86_64-redhat-linux/bits/c++config.h:2359:34: note: expanded from macro '_GLIBCXX17_DEPRECATED' 2359 | # define _GLIBCXX17_DEPRECATED [[__deprecated__]] | ^ 1 warning generated. /data/gannet/ripley/intel/oneapi/compiler/2024.2//bin/icpx -std=gnu++17 -shared -L/data/gannet/ripley/intel/oneapi/compiler/2024.1/lib -L/usr/local/gcc14/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[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/scellpam/src' make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-Intel/scellpam/src' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-Intel/scellpam/src' installing to /data/gannet/ripley/R/packages/tests-Intel/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)