############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL bcSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘bcSeq’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c CRISPR_matching.cpp -o CRISPR_matching.o In file included from helper/../structures/Trie.h:16, from helper/count.h:5, from CRISPR_matching.cpp:3: helper/../structures/NodePool.h: In member function 'void Pool::resize()': helper/../structures/NodePool.h:58:16: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from helper/../structures/Trie.h:15: helper/../structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c Trie_edit.cpp -o Trie_edit.o In file included from structures/Trie.h:16, from Trie_edit.cpp:1: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:16: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from structures/Trie.h:15: structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c Trie_hamming.cpp -o Trie_hamming.o In file included from structures/Trie.h:16, from Trie_hamming.cpp:1: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:16: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from structures/Trie.h:15: structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c Trie_util.cpp -o Trie_util.o In file included from structures/Trie.h:16, from Trie_util.cpp:2: structures/NodePool.h: In member function 'void Pool::resize()': structures/NodePool.h:58:16: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Node'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 58 | std::memcpy(x, buff.get(), count * sizeof(Node)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from structures/Trie.h:15: structures/Node.h:11:8: note: 'struct Node' declared here 11 | struct Node { | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c alignment.cpp -o alignment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c trimRead.cpp -o trimRead.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c uniqueBar.cpp -o uniqueBar.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-bcSeq/00new/bcSeq/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 (bcSeq)