############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL NetPathMiner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘NetPathMiner’ ... ** using staged installation 'config' variable 'CPP' is defunct 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 how to run the C preprocessor... gcc -E checking for xmlParseFile in -lxml2... yes checking for readSBML in -lsbml... no Non x86_64 architecture. Using system-wide boost installation! SBML not found. libXML2 found checking for xml2-config... /usr/bin/xml2-config configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c PathRanker.cpp -o PathRanker.o In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:606, from /usr/include/boost/graph/properties.hpp:19, from /usr/include/boost/graph/graph_utility.hpp:22, from PathRanker.cpp:27: /usr/include/boost/pending/relaxed_heap.hpp:14:1: note: ‘#pragma message: This header is deprecated. Use the standard heap functions instead.’ 14 | BOOST_HEADER_DEPRECATED("the standard heap functions") | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c handlesegfault.c -o handlesegfault.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c hme3m.c -o hme3m.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c kgml_interface.cpp -o kgml_interface.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c methods.cpp -o methods.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c pathScope.cpp -o pathScope.o In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:606, from /usr/include/boost/graph/properties.hpp:19, from /usr/include/boost/graph/graph_utility.hpp:22, from pathScope.cpp:34: /usr/include/boost/pending/relaxed_heap.hpp:14:1: note: ‘#pragma message: This header is deprecated. Use the standard heap functions instead.’ 14 | BOOST_HEADER_DEPRECATED("the standard heap functions") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c sbml_interface.cpp -o sbml_interface.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lxml2 -lxml2 -lz -llzma -lm -lopenblas -lgfortran -lm -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-NetPathMiner/00new/NetPathMiner/libs ** R ** data ** 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 Warning in fun(libname, pkgname) : Package 'NetPathMiner' is deprecated and will be removed from Bioconductor version 3.20 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'NetPathMiner' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (NetPathMiner)