############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SharedObject ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘SharedObject’ ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for shm_open in -lrt... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 mkdir -p ../inst/include&&\ mkdir -p ../inst/include/SharedObject&&\ mkdir -p ../inst/usrlib g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c C_interface.cpp -o C_interface.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c altrep.cpp -o altrep.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c altrepRegistration.cpp -o altrepRegistration.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c numericAltrepOperations.cpp -o numericAltrepOperations.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c sharedMemory.cpp -o sharedMemory.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c sharedObjectClass.cpp -o sharedObjectClass.o sharedObjectClass.cpp: In function ‘void validate_shared_memory(std::string, boost::interprocess::shared_memory_object*)’: sharedObjectClass.cpp:73:14: warning: comparison of integer expressions of different signedness: ‘boost::interprocess::offset_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | if (size > free_size) | ~~~~~^~~~~~~~~~~ sharedObjectClass.cpp: In member function ‘void SharedObjectClass::openSharedMemoryHandle()’: sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized] 29 | return size; | ^~~~ sharedObjectClass.cpp:27:14: note: ‘size’ was declared here 27 | offset_t size; | ^~~~ sharedObjectClass.cpp: In member function ‘size_t SharedObjectClass::getSharedMemorySize()’: sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized] 29 | return size; | ^~~~ sharedObjectClass.cpp:27:14: note: ‘size’ was declared here 27 | offset_t size; | ^~~~ sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized] 29 | return size; | ^~~~ sharedObjectClass.cpp:27:14: note: ‘size’ was declared here 27 | offset_t size; | ^~~~ sharedObjectClass.cpp: In member function ‘void SharedObjectClass::allocateSharedMemory()’: sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized] 29 | return size; | ^~~~ sharedObjectClass.cpp:27:14: note: ‘size’ was declared here 27 | offset_t size; | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c stringAltrepOperations.cpp -o stringAltrepOperations.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SharedObject.so C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o -lrt -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR ar -crv SharedObject.a *.o a - C_interface.o a - RcppExports.o a - altrep.o a - altrepRegistration.o a - numericAltrepOperations.o a - sharedMemory.o a - sharedObjectClass.o a - stringAltrepOperations.o a - utils.o cp "sharedMemory.h" "../inst/include/SharedObject/"&&\ cp "SharedObject.a" "../inst/usrlib/" installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-SharedObject/00new/SharedObject/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 (SharedObject)