############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SVP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘SVP’ ... ** this is package ‘SVP’ version ‘1.1.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:4: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c autocorutils.cpp -o autocorutils.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from autocorutils.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c bisp.cpp -o bisp.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from autocorutils.h:1, from bisp.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c cor.cpp -o cor.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from cor.cpp:2: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c extract.cpp -o extract.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from extract.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c gearysc.cpp -o gearysc.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from autocorutils.h:1, from gearysc.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c getisord.cpp -o getisord.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from getisord.cpp:2: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c kld.cpp -o kld.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from kld.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c lisa.cpp -o lisa.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from autocorutils.h:1, from lisa.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c mca.cpp -o mca.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from mca.cpp:4: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c metric.cpp -o metric.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from autocorutils.h:1, from metric.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c moransi.cpp -o moransi.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from autocorutils.h:1, from moransi.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c pairknn.cpp -o pairknn.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from pairknn.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c rwr.cpp -o rwr.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from rwr.cpp:1: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o SVP.so RcppExports.o autocorutils.o bisp.o cor.o extract.o gearysc.o getisord.o kld.o lisa.o mca.o metric.o moransi.o pairknn.o rwr.o -fopenmp -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-SVP/00new/SVP/libs ** R ** data ** 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 (SVP)