############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL beachmat ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘beachmat’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c delayed_isometric_math.cpp -o delayed_isometric_math.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c delayed_other.cpp -o delayed_other.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c dense_matrix.cpp -o dense_matrix.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c sparse_matrix.cpp -o sparse_matrix.o In file included from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/tatami.hpp:8, from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami_r/UnknownMatrix.hpp:5, from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami_r/tatami_r.hpp:4, from ../inst/include/Rtatami.h:8, from sparse_matrix.cpp:1: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool, bool) [with Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView; IndexStorage_ = tatami::ArrayView; PointerStorage_ = tatami::ArrayView]’: sparse_matrix.cpp:13:12: required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = int; XVector_ = Rcpp::Vector<10, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix; Rcpp::IntegerVector = Rcpp::Vector<13>]’ sparse_matrix.cpp:36:51: required from here /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp:534:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 534 | for (size_t j = start + 1; j < end; ++j) { | ~~^~~~~ /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool, bool) [with Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView; IndexStorage_ = tatami::ArrayView; PointerStorage_ = tatami::ArrayView]’: sparse_matrix.cpp:13:12: required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = double; XVector_ = Rcpp::Vector<14, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix; Rcpp::IntegerVector = Rcpp::Vector<13>]’ sparse_matrix.cpp:40:54: required from here /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp:534:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c tatami_utils.cpp -o tatami_utils.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c unknown_matrix.cpp -o unknown_matrix.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o beachmat.so RcppExports.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o sparse_matrix.o tatami_utils.o unknown_matrix.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-beachmat/00new/beachmat/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 (beachmat)