############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘alabaster.base’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c check_csv.cpp -o check_csv.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c check_list.cpp -o check_list.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c is_rfc3339.cpp -o is_rfc3339.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c load_csv.cpp -o load_csv.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c load_list.cpp -o load_list.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c validate.cpp -o validate.o In file included from ../inst/include/chihaya/validate.hpp:13, from ../inst/include/chihaya/chihaya.hpp:10, from ../inst/include/takane/utils_public.hpp:13, from ../inst/include/takane/_validate.hpp:9, from ../inst/include/takane/takane.hpp:4, from validate.cpp:2: ../inst/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = long unsigned int]’: ../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized in this function [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ ../inst/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = int]’: ../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized in this function [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-alabaster.base/00new/alabaster.base/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 (alabaster.base)